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man.clinicalClient-OpencgaR-method.Rd Maven / Gradle / Ivy

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Clinical-methods.R
\name{clinicalClient,OpencgaR-method}
\alias{clinicalClient,OpencgaR-method}
\title{ClinicalClient methods}
\usage{
\S4method{clinicalClient}{OpencgaR}(
  OpencgaR,
  members,
  interpretations,
  interpretation,
  clinicalAnalyses,
  clinicalAnalysis,
  endpointName,
  params = NULL,
  ...
)
}
\arguments{
\item{members}{Comma separated list of user or group IDs.}

\item{interpretations}{Interpretation IDs of the Clinical Analysis.}

\item{interpretation}{Interpretation ID.}

\item{clinicalAnalyses}{Comma separated list of clinical analysis IDs.}

\item{clinicalAnalysis}{Clinical analysis ID.}

\item{action}{Action to be performed \link{ADD, SET, REMOVE or RESET}.}

\item{propagate}{Propagate permissions to related families, individuals, samples and files.}

\item{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.}

\item{sort}{Sort the results.}

\item{clinicalAnalysisId}{Clinical Analysis id.}

\item{methodName}{Interpretation method name.}

\item{primaryFindings}{Interpretation primary findings.}

\item{secondaryFindings}{Interpretation secondary findings.}

\item{field}{List of fields separated by semicolons, e.g.: clinicalSignificances;type. For nested fields use >>, e.g.: type>>clinicalSignificances;knockoutType.}

\item{jobId}{Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.}

\item{jobDescription}{Job description.}

\item{jobDependsOn}{Comma separated list of existing job IDs the job will depend on.}

\item{jobTags}{Job tags.}

\item{auxiliarIndex}{Index auxiliar collection to improve performance assuming RGA is completely indexed.}

\item{includeIndividual}{Include only the comma separated list of individuals to the response.}

\item{skipIndividual}{Number of individuals to skip.}

\item{limitIndividual}{Limit number of individuals returned (default: 1000).}

\item{sampleId}{Filter by sample id.}

\item{individualId}{Filter by individual id.}

\item{sex}{Filter by sex.}

\item{phenotypes}{Filter by phenotypes.}

\item{disorders}{Filter by disorders.}

\item{numParents}{Filter by the number of parents registered.}

\item{geneId}{Filter by gene id.}

\item{geneName}{Filter by gene name.}

\item{chromosome}{Filter by chromosome.}

\item{start}{Filter by start position.}

\item{end}{Filter by end position.}

\item{transcriptId}{Filter by transcript id.}

\item{variants}{Filter by variant id.}

\item{dbSnps}{Filter by DB_SNP id.}

\item{knockoutType}{Filter by knockout type.}

\item{populationFrequency}{Filter by population frequency.}

\item{consequenceType}{Filter by consequence type.}

\item{uuid}{Comma separated list of Clinical Analysis UUIDs up to a maximum of 100.}

\item{disorder}{Clinical Analysis disorder.}

\item{files}{Clinical Analysis files.}

\item{individual}{Proband or any member of a family.}

\item{proband}{Clinical Analysis proband.}

\item{probandSamples}{Clinical Analysis proband samples.}

\item{familyMemberSamples}{Clinical Analysis family members samples.}

\item{panels}{Clinical Analysis panels.}

\item{locked}{Locked Clinical Analyses.}

\item{analystId}{Clinical Analysis analyst id.}

\item{priority}{Clinical Analysis priority.}

\item{flags}{Clinical Analysis flags.}

\item{creationDate}{Clinical Analysis Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.}

\item{modificationDate}{Clinical Analysis Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.}

\item{qualityControlSummary}{Clinical Analysis quality control summary.}

\item{release}{Release when it was created.}

\item{status}{Filter by status.}

\item{internalStatus}{Filter by internal status.}

\item{limit}{Number of results to be returned.}

\item{skip}{Number of results to skip.}

\item{count}{Get the total number of results matching the query. Deactivated by default.}

\item{approximateCount}{Get an approximate count, instead of an exact total count. Reduces execution time.}

\item{approximateCountSamplingSize}{Sampling size to get the approximate count. Larger values increase accuracy but also increase execution time.}

\item{savedFilter}{Use a saved filter at User level.}

\item{id}{List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt, e.g. rs116600158,19:7177679:C:T.}

\item{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.}

\item{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.}

\item{file}{Filter variants from the files specified. This will set includeFile parameter when not provided.}

\item{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.}

\item{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.}

\item{fileData}{Filter by file data (i.e. FILTER, QUAL and INFO columns from VCF file). [{file}:]{key}{op}{value}\link{,;}* . 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.}

\item{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: \link{ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous }. Value is case insensitive. e.g. HG0097:DeNovo Sample must have parents defined and indexed. .}

\item{sampleData}{Filter by any SampleData field from samples. [{sample}:]{key}{op}{value}\link{,;}* . 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.}

\item{sampleAnnotation}{Selects some samples using metadata information from Catalog. e.g. age>20;phenotype=hpo:123,hpo:456;name=smith.}

\item{cohort}{Select variants with calculated stats for the selected cohorts.}

\item{cohortStatsRef}{Reference Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.}

\item{cohortStatsAlt}{Alternate Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.}

\item{cohortStatsMaf}{Minor Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.}

\item{cohortStatsMgf}{Minor Genotype Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL<=0.4.}

\item{cohortStatsPass}{Filter PASS frequency: [{study:}]{cohort}[<|>|<=|>=]{number}. e.g. ALL>0.8.}

\item{missingAlleles}{Number of missing alleles: [{study:}]{cohort}[<|>|<=|>=]{number}.}

\item{missingGenotypes}{Number of missing genotypes: [{study:}]{cohort}[<|>|<=|>=]{number}.}

\item{score}{Filter by variant score: [{study:}]{score}[<|>|<=|>=]{number}.}

\item{family}{Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT).}

\item{familyDisorder}{Specify the disorder to use for the family segregation.}

\item{familySegregation}{Filter by segregation mode from a given family. Accepted values: \link{ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous }.}

\item{familyMembers}{Sub set of the members of a given family.}

\item{familyProband}{Specify the proband child to use for the family segregation.}

\item{gene}{List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' parameter.}

\item{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'.}

\item{xref}{List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ...}

\item{biotype}{List of biotypes, e.g. protein_coding.}

\item{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.}

\item{conservation}{Filter by conservation score: {conservation_score}[<|>|<=|>=]{number} e.g. phastCons>0.5,phylop<0.1,gerp>0.1.}

\item{populationFrequencyAlt}{Alternate Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1kG_phase3:ALL<0.01.}

\item{populationFrequencyRef}{Reference Population Frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1kG_phase3:ALL<0.01.}

\item{populationFrequencyMaf}{Population minor allele frequency: {study}:{population}[<|>|<=|>=]{number}. e.g. 1kG_phase3:ALL<0.01.}

\item{transcriptFlag}{List of transcript flags. e.g. canonical, CCDS, basic, LRG, MANE Select, MANE Plus Clinical, EGLH_HaemOnc, TSO500.}

\item{geneTraitId}{List of gene trait association id. e.g. "umls:C0007222" , "OMIM:269600".}

\item{go}{List of GO (Gene Ontology) terms. e.g. "GO:0002020".}

\item{expression}{List of tissues of interest. e.g. "lung".}

\item{proteinKeyword}{List of Uniprot protein variant annotation keywords.}

\item{drug}{List of drug names.}

\item{functionalScore}{Functional score: {functional_score}[<|>|<=|>=]{number} e.g. cadd_scaled>5.2 , cadd_raw<=0.3.}

\item{clinical}{Clinical source: clinvar, cosmic.}

\item{clinicalSignificance}{Clinical significance: benign, likely_benign, likely_pathogenic, pathogenic.}

\item{clinicalConfirmedStatus}{Clinical confirmed status.}

\item{customAnnotation}{Custom annotation: {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}.}

\item{panel}{Filter by genes from the given disease panel.}

\item{panelModeOfInheritance}{Filter genes from specific panels that match certain mode of inheritance. Accepted values : \link{ autosomalDominant, autosomalRecessive, XLinkedDominant, XLinkedRecessive, YLinked, mitochondrial, deNovo, mendelianError, compoundHeterozygous }.}

\item{panelConfidence}{Filter genes from specific panels that match certain confidence. Accepted values : \link{ high, medium, low, rejected }.}

\item{panelRoleInCancer}{Filter genes from specific panels that match certain role in cancer. Accepted values : \link{ both, oncogene, tumorSuppressorGene, fusion }.}

\item{panelFeatureType}{Filter elements from specific panels by type. Accepted values : \link{ gene, region, str, variant }.}

\item{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.}

\item{trait}{List of traits, based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies, descriptions,...}

\item{member}{User or group ID.}

\item{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.}

\item{force}{Force deletion if the ClinicalAnalysis contains interpretations or is locked.}

\item{flagsAction}{Action to be performed if the array of flags is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}

\item{filesAction}{Action to be performed if the array of files is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}

\item{deleted}{Boolean to retrieve deleted entries.}

\item{setAsPrimary}{Interpretation id to set as primary from the list of secondaries in case of deleting the actual primary one.}

\item{version}{Version to revert to.}

\item{include}{Fields included in the response, whole JSON path must be provided.}

\item{exclude}{Fields excluded in the response, whole JSON path must be provided.}

\item{study}{[\link{user@}project:]study ID.}

\item{primaryFindingsAction}{Action to be performed if the array of primary findings is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE', 'REPLACE'}}

\item{methodsAction}{Action to be performed if the array of methods is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}

\item{secondaryFindingsAction}{Action to be performed if the array of secondary findings is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE', 'REPLACE'}}

\item{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: \link{'ADD', 'REMOVE', 'REPLACE'}}

\item{panelsAction}{Action to be performed if the array of panels is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}

\item{setAs}{Set interpretation as. Allowed values: \link{'PRIMARY', 'SECONDARY'}}

\item{includeResult}{Flag indicating to include the created or updated document result in the response.}

\item{data}{JSON containing clinical interpretation information.}
}
\description{
This function implements the OpenCGA calls for managing Analysis - Clinical.
The following table summarises the available \emph{actions} for this client:\tabular{llr}{
   endpointName \tab Endpoint WS \tab parameters accepted \cr
   updateAcl \tab /{apiVersion}/analysis/clinical/acl/{members}/update \tab study, members\link{*}, action\link{*}, propagate, body\link{*} \cr
   updateClinicalConfiguration \tab /{apiVersion}/analysis/clinical/clinical/configuration/update \tab study, body \cr
   create \tab /{apiVersion}/analysis/clinical/create \tab include, exclude, study, skipCreateDefaultInterpretation, includeResult, body\link{*} \cr
   distinct \tab /{apiVersion}/analysis/clinical/distinct \tab study, id, uuid, type, disorder, files, sample, individual, proband, probandSamples, family, familyMembers, familyMemberSamples, panels, locked, analystId, priority, flags, creationDate, modificationDate, qualityControlSummary, release, status, internalStatus, deleted, field\link{*} \cr
   distinctInterpretation \tab /{apiVersion}/analysis/clinical/interpretation/distinct \tab study, id, uuid, clinicalAnalysisId, analystId, methodName, panels, primaryFindings, secondaryFindings, creationDate, modificationDate, status, internalStatus, release, field\link{*} \cr
   searchInterpretation \tab /{apiVersion}/analysis/clinical/interpretation/search \tab include, exclude, limit, skip, sort, study, id, uuid, clinicalAnalysisId, analystId, methodName, panels, primaryFindings, secondaryFindings, creationDate, modificationDate, status, internalStatus, release \cr
   infoInterpretation \tab /{apiVersion}/analysis/clinical/interpretation/{interpretations}/info \tab include, exclude, interpretations\link{*}, study, version, deleted \cr
   runInterpreterCancerTiering \tab /{apiVersion}/analysis/clinical/interpreter/cancerTiering/run \tab study, jobId, jobDescription, jobDependsOn, jobTags, body\link{*} \cr
   runInterpreterTeam \tab /{apiVersion}/analysis/clinical/interpreter/team/run \tab study, jobId, jobDescription, jobDependsOn, jobTags, body\link{*} \cr
   runInterpreterTiering \tab /{apiVersion}/analysis/clinical/interpreter/tiering/run \tab study, jobId, jobDescription, jobDependsOn, jobTags, body\link{*} \cr
   runInterpreterZetta \tab /{apiVersion}/analysis/clinical/interpreter/zetta/run \tab study, jobId, jobDescription, jobDependsOn, jobTags, body\link{*} \cr
   aggregationStatsRga \tab /{apiVersion}/analysis/clinical/rga/aggregationStats \tab limit, skip, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study, field\link{*} \cr
   queryRgaGene \tab /{apiVersion}/analysis/clinical/rga/gene/query \tab 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 \cr
   summaryRgaGene \tab /{apiVersion}/analysis/clinical/rga/gene/summary \tab limit, skip, count, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study \cr
   runRgaIndex \tab /{apiVersion}/analysis/clinical/rga/index/run \tab study, jobId, jobDescription, jobDependsOn, jobTags, auxiliarIndex, body\link{*} \cr
   queryRgaIndividual \tab /{apiVersion}/analysis/clinical/rga/individual/query \tab 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 \cr
   summaryRgaIndividual \tab /{apiVersion}/analysis/clinical/rga/individual/summary \tab limit, skip, count, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study \cr
   queryRgaVariant \tab /{apiVersion}/analysis/clinical/rga/variant/query \tab 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 \cr
   summaryRgaVariant \tab /{apiVersion}/analysis/clinical/rga/variant/summary \tab limit, skip, count, sampleId, individualId, sex, phenotypes, disorders, numParents, geneId, geneName, chromosome, start, end, transcriptId, variants, dbSnps, knockoutType, filter, type, clinicalSignificance, populationFrequency, consequenceType, study \cr
   search \tab /{apiVersion}/analysis/clinical/search \tab include, exclude, limit, skip, count, study, id, uuid, type, disorder, files, sample, individual, proband, probandSamples, family, familyMembers, familyMemberSamples, panels, locked, analystId, priority, flags, creationDate, modificationDate, qualityControlSummary, release, status, internalStatus, deleted \cr
   actionableVariant \tab /{apiVersion}/analysis/clinical/variant/actionable \tab study, sample \cr
   queryVariant \tab /{apiVersion}/analysis/clinical/variant/query \tab include, exclude, limit, skip, count, approximateCount, approximateCountSamplingSize, savedFilter, 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 \cr
   acl \tab /{apiVersion}/analysis/clinical/{clinicalAnalyses}/acl \tab clinicalAnalyses\link{*}, study, member, silent \cr
   delete \tab /{apiVersion}/analysis/clinical/{clinicalAnalyses}/delete \tab study, force, clinicalAnalyses\link{*} \cr
   update \tab /{apiVersion}/analysis/clinical/{clinicalAnalyses}/update \tab include, exclude, clinicalAnalyses\link{*}, study, commentsAction, flagsAction, filesAction, panelsAction, includeResult, body\link{*} \cr
   info \tab /{apiVersion}/analysis/clinical/{clinicalAnalysis}/info \tab include, exclude, clinicalAnalysis\link{*}, study, deleted \cr
   createInterpretation \tab /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create \tab include, exclude, clinicalAnalysis\link{*}, study, setAs, includeResult, body\link{*} \cr
   clearInterpretation \tab /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/clear \tab study, interpretations\link{*}, clinicalAnalysis\link{*} \cr
   deleteInterpretation \tab /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/delete \tab study, clinicalAnalysis\link{*}, interpretations\link{*}, setAsPrimary \cr
   revertInterpretation \tab /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/revert \tab study, clinicalAnalysis\link{*}, interpretation\link{*}, version\link{*} \cr
   updateInterpretation \tab /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update \tab include, exclude, study, primaryFindingsAction, methodsAction, secondaryFindingsAction, commentsAction, panelsAction, setAs, clinicalAnalysis\link{*}, interpretation\link{*}, includeResult, body\link{*} \cr
}
}
\section{Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update}{

Update the set of permissions granted for the member.
}

\section{Endpoint /{apiVersion}/analysis/clinical/clinical/configuration/update}{

Update Clinical Analysis configuration.
}

\section{Endpoint /{apiVersion}/analysis/clinical/create}{

Create a new clinical analysis.
}

\section{Endpoint /{apiVersion}/analysis/clinical/distinct}{

Clinical Analysis distinct method.
}

\section{Endpoint /{apiVersion}/analysis/clinical/interpretation/distinct}{

Interpretation distinct method.
}

\section{Endpoint /{apiVersion}/analysis/clinical/interpretation/search}{

Search clinical interpretations.
}

\section{Endpoint /{apiVersion}/analysis/clinical/interpretation/{interpretations}/info}{

Clinical interpretation information.
}

\section{Endpoint /{apiVersion}/analysis/clinical/interpreter/cancerTiering/run}{

Run cancer tiering interpretation analysis.
}

\section{Endpoint /{apiVersion}/analysis/clinical/interpreter/team/run}{

Run TEAM interpretation analysis.
}

\section{Endpoint /{apiVersion}/analysis/clinical/interpreter/tiering/run}{

Run tiering interpretation analysis.
}

\section{Endpoint /{apiVersion}/analysis/clinical/interpreter/zetta/run}{

Run Zetta interpretation analysis.
}

\section{Endpoint /{apiVersion}/analysis/clinical/rga/aggregationStats}{

RGA aggregation stats.
}

\section{Endpoint /{apiVersion}/analysis/clinical/rga/gene/query}{

Query gene RGA.
}

\section{Endpoint /{apiVersion}/analysis/clinical/rga/gene/summary}{

RGA gene summary stats.
}

\section{Endpoint /{apiVersion}/analysis/clinical/rga/index/run}{

Generate Recessive Gene Analysis secondary index.
}

\section{Endpoint /{apiVersion}/analysis/clinical/rga/individual/query}{

Query individual RGA.
}

\section{Endpoint /{apiVersion}/analysis/clinical/rga/individual/summary}{

RGA individual summary stats.
}

\section{Endpoint /{apiVersion}/analysis/clinical/rga/variant/query}{

Query variant RGA.
}

\section{Endpoint /{apiVersion}/analysis/clinical/rga/variant/summary}{

RGA variant summary stats.
}

\section{Endpoint /{apiVersion}/analysis/clinical/search}{

Clinical analysis search.
}

\section{Endpoint /{apiVersion}/analysis/clinical/variant/actionable}{

Fetch actionable clinical variants.
}

\section{Endpoint /{apiVersion}/analysis/clinical/variant/query}{

Fetch clinical variants.
}

\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.
}

\section{Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalyses}/delete}{

Delete clinical analyses.
}

\section{Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalyses}/update}{

Update clinical analysis attributes.
}

\section{Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/info}{

Clinical analysis info.
}

\section{Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/create}{

Create a new Interpretation.
}

\section{Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/clear}{

Clear the fields of the main interpretation of the Clinical Analysis.
}

\section{Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretations}/delete}{

Delete interpretation.
}

\section{Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/revert}{

Revert to a previous interpretation version.
}

\section{Endpoint /{apiVersion}/analysis/clinical/{clinicalAnalysis}/interpretation/{interpretation}/update}{

Update interpretation fields.
}

\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/}
\link{*}: Required parameter
}