R.Clinical-methods.R Maven / Gradle / Ivy
# WARNING: AUTOGENERATED CODE
#
# This code was generated by a tool.
#
# Manual changes to this file may cause unexpected behavior in your application.
# Manual changes to this file will be overwritten if the code is regenerated.
# ##############################################################################
#' ClinicalClient methods
#' @include AllClasses.R
#' @include AllGenerics.R
#' @include commons.R
#' @description This function implements the OpenCGA calls for managing Analysis - Clinical.
#' The following table summarises the available *actions* for this client:
#'
#' | endpointName | Endpoint WS | parameters accepted |
#' | -- | :-- | --: |
#' | updateAcl | /{apiVersion}/analysis/clinical/acl/{members}/update | study, members[*], action[*], propagate, body[*] |
#' | loadAnnotationSets | /{apiVersion}/analysis/clinical/annotationSets/load | study, variableSetId[*], path[*], parents, annotationSetId, body |
#' | updateClinicalConfiguration | /{apiVersion}/analysis/clinical/clinical/configuration/update | study, body |
#' | create | /{apiVersion}/analysis/clinical/create | include, exclude, study, skipCreateDefaultInterpretation, includeResult, body[*] |
#' | distinct | /{apiVersion}/analysis/clinical/distinct | study, id, uuid, type, disorder, files, sample, individual, proband, probandSamples, family, familyMembers, familyMemberSamples, panels, locked, analystId, priority, flags, creationDate, modificationDate, dueDate, qualityControlSummary, release, snapshot, status, internalStatus, annotation, deleted, field[*] |
#' | distinctInterpretation | /{apiVersion}/analysis/clinical/interpretation/distinct | study, id, uuid, name, clinicalAnalysisId, analystId, methodName, panels, primaryFindings, secondaryFindings, creationDate, modificationDate, status, internalStatus, release, field[*] |
#' | searchInterpretation | /{apiVersion}/analysis/clinical/interpretation/search | include, exclude, limit, skip, sort, study, id, uuid, name, clinicalAnalysisId, analystId, methodName, panels, primaryFindings, secondaryFindings, creationDate, modificationDate, status, internalStatus, release |
#' | infoInterpretation | /{apiVersion}/analysis/clinical/interpretation/{interpretations}/info | include, exclude, interpretations[*], study, version, deleted |
#' | runInterpreterCancerTiering | /{apiVersion}/analysis/clinical/interpreter/cancerTiering/run | study, jobId, jobDescription, jobDependsOn, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body[*] |
#' | runInterpreterExomiser | /{apiVersion}/analysis/clinical/interpreter/exomiser/run | study, jobId, jobDescription, jobDependsOn, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body[*] |
#' | runInterpreterTeam | /{apiVersion}/analysis/clinical/interpreter/team/run | study, jobId, jobDescription, jobDependsOn, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body[*] |
#' | runInterpreterTiering | /{apiVersion}/analysis/clinical/interpreter/tiering/run | study, jobId, jobDescription, jobDependsOn, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body[*] |
#' | runInterpreterZetta | /{apiVersion}/analysis/clinical/interpreter/zetta/run | study, jobId, jobDescription, jobDependsOn, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body[*] |
#' | load | /{apiVersion}/analysis/clinical/load | study, jobId, jobDescription, jobDependsOn, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, body[*] |
#' | aggregationStatsRga | /{apiVersion}/analysis/clinical/rga/aggregationStats | limit, skip, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study, field[*] |
#' | queryRgaGene | /{apiVersion}/analysis/clinical/rga/gene/query | include, exclude, limit, skip, count, includeIndividual, skipIndividual, limitIndividual, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study |
#' | summaryRgaGene | /{apiVersion}/analysis/clinical/rga/gene/summary | limit, skip, count, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study |
#' | runRgaIndex | /{apiVersion}/analysis/clinical/rga/index/run | study, jobId, jobDescription, jobDependsOn, jobTags, jobScheduledStartTime, jobPriority, jobDryRun, auxiliarIndex, body[*] |
#' | queryRgaIndividual | /{apiVersion}/analysis/clinical/rga/individual/query | include, exclude, limit, skip, count, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study |
#' | summaryRgaIndividual | /{apiVersion}/analysis/clinical/rga/individual/summary | limit, skip, count, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study |
#' | queryRgaVariant | /{apiVersion}/analysis/clinical/rga/variant/query | include, exclude, limit, skip, count, includeIndividual, skipIndividual, limitIndividual, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study |
#' | summaryRgaVariant | /{apiVersion}/analysis/clinical/rga/variant/summary | limit, skip, count, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study |
#' | search | /{apiVersion}/analysis/clinical/search | include, exclude, limit, skip, count, flattenAnnotations, study, id, uuid, type, disorder, files, sample, individual, proband, probandSamples, family, familyMembers, familyMemberSamples, panels, locked, analystId, priority, flags, creationDate, modificationDate, dueDate, qualityControlSummary, release, snapshot, status, internalStatus, annotation, deleted |
#' | queryVariant | /{apiVersion}/analysis/clinical/variant/query | include, exclude, limit, skip, count, approximateCount, approximateCountSamplingSize, savedFilter, includeInterpretation, id, region, type, study, file, filter, qual, fileData, sample, sampleData, sampleAnnotation, cohort, cohortStatsRef, cohortStatsAlt, cohortStatsMaf, cohortStatsMgf, cohortStatsPass, missingAlleles, missingGenotypes, score, family, familyDisorder, familySegregation, familyMembers, familyProband, gene, ct, xref, biotype, proteinSubstitution, conservation, populationFrequencyAlt, populationFrequencyRef, populationFrequencyMaf, transcriptFlag, geneTraitId, go, expression, proteinKeyword, drug, functionalScore, clinical, clinicalSignificance, clinicalConfirmedStatus, customAnnotation, panel, panelModeOfInheritance, panelConfidence, panelRoleInCancer, panelFeatureType, panelIntersection, trait |
#' | acl | /{apiVersion}/analysis/clinical/{clinicalAnalyses}/acl | clinicalAnalyses[*], study, member, silent |
#' | delete | /{apiVersion}/analysis/clinical/{clinicalAnalyses}/delete | study, force, clinicalAnalyses[*] |
#' | update | /{apiVersion}/analysis/clinical/{clinicalAnalyses}/update | include, exclude, clinicalAnalyses[*], study, commentsAction, flagsAction, analystsAction, filesAction, panelsAction, annotationSetsAction, includeResult, body[*] |
#' | updateAnnotationSetsAnnotations | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/annotationSets/{annotationSet}/annotations/update | clinicalAnalysis[*], study, annotationSet[*], action, body |
#' | info | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/info | include, exclude, flattenAnnotations, clinicalAnalysis[*], study, version, deleted |
#' | createInterpretation | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create | include, exclude, clinicalAnalysis[*], study, setAs, includeResult, body[*] |
#' | clearInterpretation | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/clear | study, interpretations[*], clinicalAnalysis[*] |
#' | deleteInterpretation | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/delete | study, clinicalAnalysis[*], interpretations[*], setAsPrimary |
#' | revertInterpretation | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/revert | study, clinicalAnalysis[*], interpretation[*], version[*] |
#' | updateInterpretation | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update | include, exclude, study, primaryFindingsAction, methodsAction, secondaryFindingsAction, commentsAction, panelsAction, setAs, clinicalAnalysis[*], interpretation[*], includeResult, body[*] |
#' | updateReport | /{apiVersion}/analysis/clinical/{clinicalAnalysis}/report/update | include, exclude, clinicalAnalysis[*], study, commentsAction, supportingEvidencesAction, filesAction, includeResult, body[*] |
#'
#' @md
#' @seealso \url{http://docs.opencb.org/display/opencga/Using+OpenCGA} and the RESTful API documentation
#' \url{http://bioinfo.hpc.cam.ac.uk/opencga-prod/webservices/}
#' [*]: Required parameter
#' @export
setMethod("clinicalClient", "OpencgaR", function(OpencgaR, annotationSet, clinicalAnalyses, clinicalAnalysis, interpretation, interpretations, members, endpointName, params=NULL, ...) {
switch(endpointName,
#' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update:
#' Update the set of permissions granted for the member.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param members Comma separated list of user or group IDs.
#' @param action Action to be performed [ADD, SET, REMOVE or RESET]. Allowed values: ['SET ADD REMOVE RESET']
#' @param propagate Propagate permissions to related families, individuals, samples and files.
#' @param data JSON containing the parameters to add ACLs.
updateAcl=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical/acl",
subcategoryId=members, action="update", params=params, httpMethod="POST", as.queryParam=c("action"),
...),
#' @section Endpoint /{apiVersion}/analysis/clinical/annotationSets/load:
#' Load annotation sets from a TSV file.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param variableSetId Variable set ID or name.
#' @param path Path where the TSV file is located in OpenCGA or where it should be located.
#' @param parents Flag indicating whether to create parent directories if they don't exist (only when TSV file was not previously associated).
#' @param annotationSetId Annotation set id. If not provided, variableSetId will be used.
#' @param data JSON containing the 'content' of the TSV file if this has not yet been registered into OpenCGA.
loadAnnotationSets=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/annotationSets", subcategoryId=NULL, action="load", params=params,
httpMethod="POST", as.queryParam=c("variableSetId","path"), ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/clinical/configuration/update:
#' Update Clinical Analysis configuration.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param data Configuration params to update.
updateClinicalConfiguration=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/clinical/configuration", subcategoryId=NULL, action="update", params=params,
httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/create:
#' Create a new clinical analysis.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param skipCreateDefaultInterpretation Flag to skip creating and initialise an empty default primary interpretation (Id will be '{clinicalAnalysisId}.1'). This flag is only considered if no Interpretation object is passed.
#' @param includeResult Flag indicating to include the created or updated document result in the response.
#' @param data JSON containing clinical analysis information.
create=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
subcategoryId=NULL, action="create", params=params, httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/distinct:
#' Clinical Analysis distinct method.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param uuid Comma separated list of Clinical Analysis UUIDs up to a maximum of 100.
#' @param type Clinical Analysis type.
#' @param disorder Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param files Clinical Analysis files.
#' @param sample Sample associated to the proband or any member of a family.
#' @param individual Proband or any member of a family.
#' @param proband Clinical Analysis proband.
#' @param probandSamples Clinical Analysis proband samples.
#' @param family Clinical Analysis family.
#' @param familyMembers Clinical Analysis family members.
#' @param familyMemberSamples Clinical Analysis family members samples.
#' @param panels Clinical Analysis panels.
#' @param locked Locked Clinical Analyses.
#' @param analystId Clinical Analysis analyst id.
#' @param priority Clinical Analysis priority.
#' @param flags Clinical Analysis flags.
#' @param creationDate Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param modificationDate Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param dueDate Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param qualityControlSummary Clinical Analysis quality control summary.
#' @param release Release when it was created.
#' @param snapshot Snapshot value (Latest version of the entry in the specified release).
#' @param status Filter by status.
#' @param internalStatus Filter by internal status.
#' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
#' @param deleted Boolean to retrieve deleted entries.
#' @param field Comma separated list of fields for which to obtain the distinct values.
distinct=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
subcategoryId=NULL, action="distinct", params=params, httpMethod="GET", as.queryParam=c("field"), ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/interpretation/distinct:
#' Interpretation distinct method.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param id Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param uuid Comma separated list of Interpretation UUIDs up to a maximum of 100.
#' @param name Comma separated list of Interpretation names up to a maximum of 100.
#' @param clinicalAnalysisId Clinical Analysis id.
#' @param analystId Analyst ID.
#' @param methodName Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param panels Interpretation panels.
#' @param primaryFindings Interpretation primary findings.
#' @param secondaryFindings Interpretation secondary findings.
#' @param creationDate Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param modificationDate Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param status Filter by status.
#' @param internalStatus Filter by internal status.
#' @param release Release when it was created.
#' @param field Comma separated list of fields for which to obtain the distinct values.
distinctInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/interpretation", subcategoryId=NULL, action="distinct", params=params,
httpMethod="GET", as.queryParam=c("field"), ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/interpretation/search:
#' Search clinical interpretations.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param sort Sort the results.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param id Comma separated list of Interpretation IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param uuid Comma separated list of Interpretation UUIDs up to a maximum of 100.
#' @param name Comma separated list of Interpretation names up to a maximum of 100.
#' @param clinicalAnalysisId Clinical Analysis id.
#' @param analystId Analyst ID.
#' @param methodName Interpretation method name. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param panels Interpretation panels.
#' @param primaryFindings Interpretation primary findings.
#' @param secondaryFindings Interpretation secondary findings.
#' @param creationDate Interpretation Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param modificationDate Interpretation Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param status Filter by status.
#' @param internalStatus Filter by internal status.
#' @param release Release when it was created.
searchInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/interpretation", subcategoryId=NULL, action="search", params=params,
httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/interpretation/{interpretations}/info:
#' Clinical interpretation information.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param interpretations Comma separated list of clinical interpretation IDs up to a maximum of 100.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param version Comma separated list of interpretation versions. 'all' to get all the interpretation versions. Not supported if multiple interpretation ids are provided.
#' @param deleted Boolean to retrieve deleted entries.
infoInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/interpretation", subcategoryId=interpretations, action="info", params=params,
httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/interpreter/cancerTiering/run:
#' Run cancer tiering interpretation analysis.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
#' @param jobDescription Job description.
#' @param jobDependsOn Comma separated list of existing job IDs the job will depend on.
#' @param jobTags Job tags.
#' @param jobScheduledStartTime Time when the job is scheduled to start.
#' @param jobPriority Priority of the job.
#' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
#' @param data Cancer tiering interpretation analysis params.
runInterpreterCancerTiering=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/interpreter/cancerTiering", subcategoryId=NULL, action="run", params=params,
httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/interpreter/exomiser/run:
#' Run exomiser interpretation analysis.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
#' @param jobDescription Job description.
#' @param jobDependsOn Comma separated list of existing job IDs the job will depend on.
#' @param jobTags Job tags.
#' @param jobScheduledStartTime Time when the job is scheduled to start.
#' @param jobPriority Priority of the job.
#' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
#' @param data Exomiser interpretation analysis params.
runInterpreterExomiser=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/interpreter/exomiser", subcategoryId=NULL, action="run", params=params,
httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/interpreter/team/run:
#' Run TEAM interpretation analysis.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
#' @param jobDescription Job description.
#' @param jobDependsOn Comma separated list of existing job IDs the job will depend on.
#' @param jobTags Job tags.
#' @param jobScheduledStartTime Time when the job is scheduled to start.
#' @param jobPriority Priority of the job.
#' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
#' @param data TEAM interpretation analysis params.
runInterpreterTeam=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/interpreter/team", subcategoryId=NULL, action="run", params=params,
httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/interpreter/tiering/run:
#' Run tiering interpretation analysis.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
#' @param jobDescription Job description.
#' @param jobDependsOn Comma separated list of existing job IDs the job will depend on.
#' @param jobTags Job tags.
#' @param jobScheduledStartTime Time when the job is scheduled to start.
#' @param jobPriority Priority of the job.
#' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
#' @param data Tiering interpretation analysis params.
runInterpreterTiering=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/interpreter/tiering", subcategoryId=NULL, action="run", params=params,
httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/interpreter/zetta/run:
#' Run Zetta interpretation analysis.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
#' @param jobDescription Job description.
#' @param jobDependsOn Comma separated list of existing job IDs the job will depend on.
#' @param jobTags Job tags.
#' @param jobScheduledStartTime Time when the job is scheduled to start.
#' @param jobPriority Priority of the job.
#' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
#' @param data Zetta interpretation analysis params.
runInterpreterZetta=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/interpreter/zetta", subcategoryId=NULL, action="run", params=params,
httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/load:
#' Load clinical analyses from a file.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
#' @param jobDescription Job description.
#' @param jobDependsOn Comma separated list of existing job IDs the job will depend on.
#' @param jobTags Job tags.
#' @param jobScheduledStartTime Time when the job is scheduled to start.
#' @param jobPriority Priority of the job.
#' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
#' @param data Parameters to load clinical analysis in OpenCGA catalog from a file.
load=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
subcategoryId=NULL, action="load", params=params, httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/rga/aggregationStats:
#' RGA aggregation stats.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param sampleId Filter by sample id.
#' @param individualId Filter by individual id.
#' @param sex Filter by sex.
#' @param phenotypes Filter by phenotypes.
#' @param disorders Filter by disorders.
#' @param numParents Filter by the number of parents registered.
#' @param geneId Filter by gene id.
#' @param geneName Filter by gene name.
#' @param chromosome Filter by chromosome.
#' @param start Filter by start position.
#' @param end Filter by end position.
#' @param transcriptId Filter by transcript id.
#' @param variants Filter by variant id.
#' @param dbSnps Filter by DB_SNP id.
#' @param knockoutType Filter by knockout type.
#' @param filter Filter by filter (PASS, NOT_PASS).
#' @param type Filter by variant type.
#' @param clinicalSignificance Filter by clinical significance.
#' @param populationFrequency Filter by population frequency.
#' @param consequenceType Filter by consequence type.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param field List of fields separated by semicolons, e.g.: clinicalSignificances;type. For nested fields use >>, e.g.: type>>clinicalSignificances;knockoutType.
aggregationStatsRga=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/rga", subcategoryId=NULL, action="aggregationStats", params=params,
httpMethod="GET", as.queryParam=c("field"), ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/rga/gene/query:
#' Query gene RGA.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param count Get the total number of results matching the query. Deactivated by default.
#' @param includeIndividual Include only the comma separated list of individuals to the response.
#' @param skipIndividual Number of individuals to skip.
#' @param limitIndividual Limit number of individuals returned (default: 1000).
#' @param sampleId Filter by sample id.
#' @param individualId Filter by individual id.
#' @param sex Filter by sex.
#' @param phenotypes Filter by phenotypes.
#' @param disorders Filter by disorders.
#' @param numParents Filter by the number of parents registered.
#' @param geneId Filter by gene id.
#' @param geneName Filter by gene name.
#' @param chromosome Filter by chromosome.
#' @param start Filter by start position.
#' @param end Filter by end position.
#' @param transcriptId Filter by transcript id.
#' @param variants Filter by variant id.
#' @param dbSnps Filter by DB_SNP id.
#' @param knockoutType Filter by knockout type.
#' @param filter Filter by filter (PASS, NOT_PASS).
#' @param type Filter by variant type.
#' @param clinicalSignificance Filter by clinical significance.
#' @param populationFrequency Filter by population frequency.
#' @param consequenceType Filter by consequence type.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
queryRgaGene=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/rga/gene", subcategoryId=NULL, action="query", params=params, httpMethod="GET",
as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/rga/gene/summary:
#' RGA gene summary stats.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param count Get the total number of results matching the query. Deactivated by default.
#' @param sampleId Filter by sample id.
#' @param individualId Filter by individual id.
#' @param sex Filter by sex.
#' @param phenotypes Filter by phenotypes.
#' @param disorders Filter by disorders.
#' @param numParents Filter by the number of parents registered.
#' @param geneId Filter by gene id.
#' @param geneName Filter by gene name.
#' @param chromosome Filter by chromosome.
#' @param start Filter by start position.
#' @param end Filter by end position.
#' @param transcriptId Filter by transcript id.
#' @param variants Filter by variant id.
#' @param dbSnps Filter by DB_SNP id.
#' @param knockoutType Filter by knockout type.
#' @param filter Filter by filter (PASS, NOT_PASS).
#' @param type Filter by variant type.
#' @param clinicalSignificance Filter by clinical significance.
#' @param populationFrequency Filter by population frequency.
#' @param consequenceType Filter by consequence type.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
summaryRgaGene=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/rga/gene", subcategoryId=NULL, action="summary", params=params, httpMethod="GET",
as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/rga/index/run:
#' Generate Recessive Gene Analysis secondary index.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
#' @param jobDescription Job description.
#' @param jobDependsOn Comma separated list of existing job IDs the job will depend on.
#' @param jobTags Job tags.
#' @param jobScheduledStartTime Time when the job is scheduled to start.
#' @param jobPriority Priority of the job.
#' @param jobDryRun Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
#' @param auxiliarIndex Index auxiliar collection to improve performance assuming RGA is completely indexed.
#' @param data Recessive Gene Analysis index params.
runRgaIndex=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/rga/index", subcategoryId=NULL, action="run", params=params, httpMethod="POST",
as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/rga/individual/query:
#' Query individual RGA.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param count Get the total number of results matching the query. Deactivated by default.
#' @param sampleId Filter by sample id.
#' @param individualId Filter by individual id.
#' @param sex Filter by sex.
#' @param phenotypes Filter by phenotypes.
#' @param disorders Filter by disorders.
#' @param numParents Filter by the number of parents registered.
#' @param geneId Filter by gene id.
#' @param geneName Filter by gene name.
#' @param chromosome Filter by chromosome.
#' @param start Filter by start position.
#' @param end Filter by end position.
#' @param transcriptId Filter by transcript id.
#' @param variants Filter by variant id.
#' @param dbSnps Filter by DB_SNP id.
#' @param knockoutType Filter by knockout type.
#' @param filter Filter by filter (PASS, NOT_PASS).
#' @param type Filter by variant type.
#' @param clinicalSignificance Filter by clinical significance.
#' @param populationFrequency Filter by population frequency.
#' @param consequenceType Filter by consequence type.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
queryRgaIndividual=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/rga/individual", subcategoryId=NULL, action="query", params=params,
httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/rga/individual/summary:
#' RGA individual summary stats.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param count Get the total number of results matching the query. Deactivated by default.
#' @param sampleId Filter by sample id.
#' @param individualId Filter by individual id.
#' @param sex Filter by sex.
#' @param phenotypes Filter by phenotypes.
#' @param disorders Filter by disorders.
#' @param numParents Filter by the number of parents registered.
#' @param geneId Filter by gene id.
#' @param geneName Filter by gene name.
#' @param chromosome Filter by chromosome.
#' @param start Filter by start position.
#' @param end Filter by end position.
#' @param transcriptId Filter by transcript id.
#' @param variants Filter by variant id.
#' @param dbSnps Filter by DB_SNP id.
#' @param knockoutType Filter by knockout type.
#' @param filter Filter by filter (PASS, NOT_PASS).
#' @param type Filter by variant type.
#' @param clinicalSignificance Filter by clinical significance.
#' @param populationFrequency Filter by population frequency.
#' @param consequenceType Filter by consequence type.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
summaryRgaIndividual=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/rga/individual", subcategoryId=NULL, action="summary", params=params,
httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/rga/variant/query:
#' Query variant RGA.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param count Get the total number of results matching the query. Deactivated by default.
#' @param includeIndividual Include only the comma separated list of individuals to the response.
#' @param skipIndividual Number of individuals to skip.
#' @param limitIndividual Limit number of individuals returned (default: 1000).
#' @param sampleId Filter by sample id.
#' @param individualId Filter by individual id.
#' @param sex Filter by sex.
#' @param phenotypes Filter by phenotypes.
#' @param disorders Filter by disorders.
#' @param numParents Filter by the number of parents registered.
#' @param geneId Filter by gene id.
#' @param geneName Filter by gene name.
#' @param chromosome Filter by chromosome.
#' @param start Filter by start position.
#' @param end Filter by end position.
#' @param transcriptId Filter by transcript id.
#' @param variants Filter by variant id.
#' @param dbSnps Filter by DB_SNP id.
#' @param knockoutType Filter by knockout type.
#' @param filter Filter by filter (PASS, NOT_PASS).
#' @param type Filter by variant type.
#' @param clinicalSignificance Filter by clinical significance.
#' @param populationFrequency Filter by population frequency.
#' @param consequenceType Filter by consequence type.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
queryRgaVariant=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/rga/variant", subcategoryId=NULL, action="query", params=params,
httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/rga/variant/summary:
#' RGA variant summary stats.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param count Get the total number of results matching the query. Deactivated by default.
#' @param sampleId Filter by sample id.
#' @param individualId Filter by individual id.
#' @param sex Filter by sex.
#' @param phenotypes Filter by phenotypes.
#' @param disorders Filter by disorders.
#' @param numParents Filter by the number of parents registered.
#' @param geneId Filter by gene id.
#' @param geneName Filter by gene name.
#' @param chromosome Filter by chromosome.
#' @param start Filter by start position.
#' @param end Filter by end position.
#' @param transcriptId Filter by transcript id.
#' @param variants Filter by variant id.
#' @param dbSnps Filter by DB_SNP id.
#' @param knockoutType Filter by knockout type.
#' @param filter Filter by filter (PASS, NOT_PASS).
#' @param type Filter by variant type.
#' @param clinicalSignificance Filter by clinical significance.
#' @param populationFrequency Filter by population frequency.
#' @param consequenceType Filter by consequence type.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
summaryRgaVariant=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/rga/variant", subcategoryId=NULL, action="summary", params=params,
httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/search:
#' Clinical analysis search.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param count Get the total number of results matching the query. Deactivated by default.
#' @param flattenAnnotations Flatten the annotations?.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param id Comma separated list of Clinical Analysis IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param uuid Comma separated list of Clinical Analysis UUIDs up to a maximum of 100.
#' @param type Clinical Analysis type.
#' @param disorder Clinical Analysis disorder. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
#' @param files Clinical Analysis files.
#' @param sample Sample associated to the proband or any member of a family.
#' @param individual Proband or any member of a family.
#' @param proband Clinical Analysis proband.
#' @param probandSamples Clinical Analysis proband samples.
#' @param family Clinical Analysis family.
#' @param familyMembers Clinical Analysis family members.
#' @param familyMemberSamples Clinical Analysis family members samples.
#' @param panels Clinical Analysis panels.
#' @param locked Locked Clinical Analyses.
#' @param analystId Clinical Analysis analyst id.
#' @param priority Clinical Analysis priority.
#' @param flags Clinical Analysis flags.
#' @param creationDate Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param modificationDate Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param dueDate Clinical Analysis due date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
#' @param qualityControlSummary Clinical Analysis quality control summary.
#' @param release Release when it was created.
#' @param snapshot Snapshot value (Latest version of the entry in the specified release).
#' @param status Filter by status.
#' @param internalStatus Filter by internal status.
#' @param annotation Annotation filters. Example: age>30;gender=FEMALE. For more information, please visit http://docs.opencb.org/display/opencga/AnnotationSets+1.4.0.
#' @param deleted Boolean to retrieve deleted entries.
search=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
subcategoryId=NULL, action="search", params=params, httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/variant/query:
#' Fetch clinical variants.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param limit Number of results to be returned.
#' @param skip Number of results to skip.
#' @param count Get the total number of results matching the query. Deactivated by default.
#' @param approximateCount Get an approximate count, instead of an exact total count. Reduces execution time.
#' @param approximateCountSamplingSize Sampling size to get the approximate count. Larger values increase accuracy but also increase execution time.
#' @param savedFilter Use a saved filter at User level.
#' @param includeInterpretation Interpretation ID to include the fields related to this interpretation.
#' @param id List of variant IDs in the format chrom:start:ref:alt, e.g. 19:7177679:C:T.
#' @param region List of regions, these can be just a single chromosome name or regions in the format chr:start-end, e.g.: 2,3:100000-200000.
#' @param type List of types, accepted values are SNV, MNV, INDEL, SV, COPY_NUMBER, COPY_NUMBER_LOSS, COPY_NUMBER_GAIN, INSERTION, DELETION, DUPLICATION, TANDEM_DUPLICATION, BREAKEND, e.g. SNV,INDEL.
#' @param study Filter variants from the given studies, these can be either the numeric ID or the alias with the format organization@project:study.
#' @param file Filter variants from the files specified. This will set includeFile parameter when not provided.
#' @param filter Specify the FILTER for any of the files. If 'file' filter is provided, will match the file and the filter. e.g.: PASS,LowGQX.
#' @param qual Specify the QUAL for any of the files. If 'file' filter is provided, will match the file and the qual. e.g.: >123.4.
#' @param fileData Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). [{file}:]{key}{op}{value}[,;]* . If no file is specified, will use all files from "file" filter. e.g. AN>200 or file_1.vcf:AN>200;file_2.vcf:AN<10 . Many fields can be combined. e.g. file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10,FILTER=PASS,LowDP.
#' @param sample Filter variants by sample genotype. This will automatically set 'includeSample' parameter when not provided. This filter accepts multiple 3 forms: 1) List of samples: Samples that contain the main variant. Accepts AND (;) and OR (,) operators. e.g. HG0097,HG0098 . 2) List of samples with genotypes: {sample}:{gt1},{gt2}. Accepts AND (;) and OR (,) operators. e.g. HG0097:0/0;HG0098:0/1,1/1 . Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa. When filtering by multi-allelic genotypes, any secondary allele will match, regardless of its position e.g. 1/2 will match with genotypes 1/2, 1/3, 1/4, .... Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT, HET_MISS and MISS e.g. HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT . 3) Sample with segregation mode: {sample}:{segregation}. Only one sample accepted.Accepted segregation modes: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ]. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. .
#' @param sampleData Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}[,;]* . If no sample is specified, will use all samples from "sample" or "genotype" filter. e.g. DP>200 or HG0097:DP>200,HG0098:DP<10 . Many FORMAT fields can be combined. e.g. HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10.
#' @param sampleAnnotation Selects some samples using metadata information from Catalog. e.g. age>20;phenotype=hpo:123,hpo:456;name=smith.
#' @param cohort Select variants with calculated stats for the selected cohorts.
#' @param cohortStatsRef Reference Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
#' @param cohortStatsAlt Alternate Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
#' @param cohortStatsMaf Minor Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
#' @param cohortStatsMgf Minor Genotype Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.
#' @param cohortStatsPass Filter PASS frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.
#' @param missingAlleles Number of missing alleles: [{study:}]{cohort}[<|>|<=|>=]{number}.
#' @param missingGenotypes Number of missing genotypes: [{study:}]{cohort}[<|>|<=|>=]{number}.
#' @param score Filter by variant score: [{study:}]{score}[<|>|<=|>=]{number}.
#' @param family Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT).
#' @param familyDisorder Specify the disorder to use for the family segregation.
#' @param familySegregation Filter by segregation mode from a given family. Accepted values: [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, deNovoStrict, mendelianError, compoundHeterozygous ].
#' @param familyMembers Sub set of the members of a given family.
#' @param familyProband Specify the proband child to use for the family segregation.
#' @param gene List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' parameter.
#' @param ct List of SO consequence types, e.g. missense_variant,stop_lost or SO:0001583,SO:0001578. Accepts aliases 'loss_of_function' and 'protein_altering'.
#' @param xref List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, HGVS ...
#' @param biotype List of biotypes, e.g. protein_coding.
#' @param proteinSubstitution Protein substitution scores include SIFT and PolyPhen. You can query using the score {protein_score}[<|>|<=|>=]{number} or the description {protein_score}[~=|=]{description} e.g. polyphen>0.1,sift=tolerant.
#' @param conservation Filter by conservation score: {conservation_score}[<|>|<=|>=]{number} e.g. phastCons>0.5,phylop<0.1,gerp>0.1.
#' @param populationFrequencyAlt Alternate Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
#' @param populationFrequencyRef Reference Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
#' @param populationFrequencyMaf Population minor allele frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1000G:ALL<0.01.
#' @param transcriptFlag List of transcript flags. e.g. canonical, CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.
#' @param geneTraitId List of gene trait association id. e.g. "umls:C0007222" , "OMIM:269600".
#' @param go List of GO (Gene Ontology) terms. e.g. "GO:0002020".
#' @param expression List of tissues of interest. e.g. "lung".
#' @param proteinKeyword List of Uniprot protein variant annotation keywords.
#' @param drug List of drug names.
#' @param functionalScore Functional score: {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 , cadd_raw<=0.3.
#' @param clinical Clinical source: clinvar, cosmic.
#' @param clinicalSignificance Clinical significance: benign, likely_benign, likely_pathogenic, pathogenic.
#' @param clinicalConfirmedStatus Clinical confirmed status.
#' @param customAnnotation Custom annotation: {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}.
#' @param panel Filter by genes from the given disease panel.
#' @param panelModeOfInheritance Filter genes from specific panels that match certain mode of inheritance. Accepted values : [ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous ].
#' @param panelConfidence Filter genes from specific panels that match certain confidence. Accepted values : [ high, medium, low, rejected ].
#' @param panelRoleInCancer Filter genes from specific panels that match certain role in cancer. Accepted values : [ both, oncogene, tumorSuppressorGene, fusion ].
#' @param panelFeatureType Filter elements from specific panels by type. Accepted values : [ gene, region, str, variant ].
#' @param panelIntersection Intersect panel genes and regions with given genes and regions from que input query. This will prevent returning variants from regions out of the panel.
#' @param trait List of traits, based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies, descriptions,...
queryVariant=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL,
subcategory="clinical/variant", subcategoryId=NULL, action="query", params=params, httpMethod="GET",
as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalyses}/acl:
#' Returns the acl of the clinical analyses. If member is provided, it will only return the acl for the member.
#' @param clinicalAnalyses Comma separated list of clinical analysis IDs or names up to a maximum of 100.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param member User or group ID.
#' @param silent Boolean to retrieve all possible entries that are queried for, false to raise an exception whenever one of the entries looked for cannot be shown for whichever reason.
acl=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
subcategoryId=clinicalAnalyses, action="acl", params=params, httpMethod="GET", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalyses}/delete:
#' Delete clinical analyses.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param force Force deletion if the ClinicalAnalysis contains interpretations or is locked.
#' @param clinicalAnalyses Comma separated list of clinical analysis IDs or names up to a maximum of 100.
delete=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
subcategoryId=clinicalAnalyses, action="delete", params=params, httpMethod="DELETE",
as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalyses}/update:
#' Update clinical analysis attributes.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param clinicalAnalyses Comma separated list of clinical analysis IDs.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param commentsAction Action to be performed if the array of comments is being updated. Allowed values: ['ADD REMOVE REPLACE']
#' @param flagsAction Action to be performed if the array of flags is being updated. Allowed values: ['ADD SET REMOVE']
#' @param analystsAction Action to be performed if the array of analysts is being updated. Allowed values: ['ADD SET REMOVE']
#' @param filesAction Action to be performed if the array of files is being updated. Allowed values: ['ADD SET REMOVE']
#' @param panelsAction Action to be performed if the array of panels is being updated. Allowed values: ['ADD SET REMOVE']
#' @param annotationSetsAction Action to be performed if the array of annotationSets is being updated. Allowed values: ['ADD SET REMOVE']
#' @param includeResult Flag indicating to include the created or updated document result in the response.
#' @param data JSON containing clinical analysis information.
update=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
subcategoryId=clinicalAnalyses, action="update", params=params, httpMethod="POST", as.queryParam=NULL,
...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/annotationSets/{annotationSet}/annotations/update:
#' Update annotations from an annotationSet.
#' @param clinicalAnalysis Clinical analysis ID.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param annotationSet AnnotationSet ID to be updated.
#' @param action Action to be performed: ADD to add new annotations; REPLACE to replace the value of an already existing annotation; SET to set the new list of annotations removing any possible old annotations; REMOVE to remove some annotations; RESET to set some annotations to the default value configured in the corresponding variables of the VariableSet if any. Allowed values: ['ADD SET REMOVE RESET REPLACE']
#' @param data Json containing the map of annotations when the action is ADD, SET or REPLACE, a json with only the key 'remove' containing the comma separated variables to be removed as a value when the action is REMOVE or a json with only the key 'reset' containing the comma separated variables that will be set to the default value when the action is RESET.
updateAnnotationSetsAnnotations=fetchOpenCGA(object=OpencgaR, category="analysis/clinical",
categoryId=clinicalAnalysis, subcategory="annotationSets", subcategoryId=annotationSet,
action="annotations/update", params=params, httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/info:
#' Clinical analysis info.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param flattenAnnotations Flatten the annotations?.
#' @param clinicalAnalysis Comma separated list of clinical analysis IDs or names up to a maximum of 100.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param version Comma separated list of clinical versions. 'all' to get all the clinical versions. Not supported if multiple clinical ids are provided.
#' @param deleted Boolean to retrieve deleted entries.
info=fetchOpenCGA(object=OpencgaR, category="analysis", categoryId=NULL, subcategory="clinical",
subcategoryId=clinicalAnalysis, action="info", params=params, httpMethod="GET", as.queryParam=NULL,
...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create:
#' Create a new Interpretation.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param clinicalAnalysis Clinical analysis ID.
#' @param study [[organization@]project:]study id.
#' @param setAs Set interpretation as. Allowed values: ['PRIMARY SECONDARY']
#' @param includeResult Flag indicating to include the created or updated document result in the response.
#' @param data JSON containing clinical interpretation information.
createInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis/clinical", categoryId=clinicalAnalysis,
subcategory="interpretation", subcategoryId=NULL, action="create", params=params, httpMethod="POST",
as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/clear:
#' Clear the fields of the main interpretation of the Clinical Analysis.
#' @param study [[organization@]project:]study ID.
#' @param interpretations Interpretation IDs of the Clinical Analysis.
#' @param clinicalAnalysis Clinical analysis ID.
clearInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis/clinical", categoryId=clinicalAnalysis,
subcategory="interpretation", subcategoryId=interpretations, action="clear", params=params,
httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/delete:
#' Delete interpretation.
#' @param study [[organization@]project:]study ID.
#' @param clinicalAnalysis Clinical analysis ID.
#' @param interpretations Interpretation IDs of the Clinical Analysis.
#' @param setAsPrimary Interpretation id to set as primary from the list of secondaries in case of deleting the actual primary one.
deleteInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis/clinical", categoryId=clinicalAnalysis,
subcategory="interpretation", subcategoryId=interpretations, action="delete", params=params,
httpMethod="DELETE", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/revert:
#' Revert to a previous interpretation version.
#' @param study [[organization@]project:]study ID.
#' @param clinicalAnalysis Clinical analysis ID.
#' @param interpretation Interpretation ID.
#' @param version Version to revert to.
revertInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis/clinical", categoryId=clinicalAnalysis,
subcategory="interpretation", subcategoryId=interpretation, action="revert", params=params,
httpMethod="POST", as.queryParam=c("version"), ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update:
#' Update interpretation fields.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param study [[organization@]project:]study ID.
#' @param primaryFindingsAction Action to be performed if the array of primary findings is being updated. Allowed values: ['ADD SET REMOVE REPLACE']
#' @param methodsAction Action to be performed if the array of methods is being updated. Allowed values: ['ADD SET REMOVE']
#' @param secondaryFindingsAction Action to be performed if the array of secondary findings is being updated. Allowed values: ['ADD SET REMOVE REPLACE']
#' @param commentsAction Action to be performed if the array of comments is being updated. To REMOVE or REPLACE, the date will need to be provided to identify the comment. Allowed values: ['ADD REMOVE REPLACE']
#' @param panelsAction Action to be performed if the array of panels is being updated. Allowed values: ['ADD SET REMOVE']
#' @param setAs Set interpretation as. Allowed values: ['PRIMARY SECONDARY']
#' @param clinicalAnalysis Clinical analysis ID.
#' @param interpretation Interpretation ID.
#' @param includeResult Flag indicating to include the created or updated document result in the response.
#' @param data JSON containing clinical interpretation information.
updateInterpretation=fetchOpenCGA(object=OpencgaR, category="analysis/clinical", categoryId=clinicalAnalysis,
subcategory="interpretation", subcategoryId=interpretation, action="update", params=params,
httpMethod="POST", as.queryParam=NULL, ...),
#' @section Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/report/update:
#' Update clinical analysis report.
#' @param include Fields included in the response, whole JSON path must be provided.
#' @param exclude Fields excluded in the response, whole JSON path must be provided.
#' @param clinicalAnalysis Clinical analysis ID.
#' @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
#' @param commentsAction Action to be performed if the array of comments is being updated. Allowed values: ['ADD REMOVE REPLACE']
#' @param supportingEvidencesAction Action to be performed if the array of supporting evidences is being updated. Allowed values: ['ADD SET REMOVE']
#' @param filesAction Action to be performed if the array of files is being updated. Allowed values: ['ADD SET REMOVE']
#' @param includeResult Flag indicating to include the created or updated document result in the response.
#' @param data JSON containing clinical report information.
updateReport=fetchOpenCGA(object=OpencgaR, category="analysis/clinical", categoryId=clinicalAnalysis,
subcategory="report", subcategoryId=NULL, action="update", params=params, httpMethod="POST",
as.queryParam=NULL, ...),
)
})© 2015 - 2025 Weber Informatics LLC | Privacy Policy