man.cohortClient-OpencgaR-method.Rd Maven / Gradle / Ivy
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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Cohort-methods.R
\name{cohortClient,OpencgaR-method}
\alias{cohortClient,OpencgaR-method}
\title{CohortClient methods}
\usage{
\S4method{cohortClient}{OpencgaR}(
OpencgaR,
members,
annotationSet,
cohorts,
cohort,
endpointName,
params = NULL,
...
)
}
\arguments{
\item{members}{Comma separated list of user or group ids.}
\item{annotationSet}{AnnotationSet ID to be updated.}
\item{cohorts}{Comma separated list of cohort ids.}
\item{cohort}{Cohort ID.}
\item{creationYear}{Creation year.}
\item{creationMonth}{Creation month (JANUARY, FEBRUARY...).}
\item{creationDay}{Creation day.}
\item{creationDayOfWeek}{Creation day of week (MONDAY, TUESDAY...).}
\item{default}{Calculate default stats.}
\item{variableSetId}{Variable set ID or name.}
\item{path}{Path where the TSV file is located in OpenCGA or where it should be located.}
\item{parents}{Flag indicating whether to create parent directories if they don't exist (only when TSV file was not previously associated).}
\item{annotationSetId}{Annotation set id. If not provided, variableSetId will be used.}
\item{variableSet}{Deprecated: Use /generate web service and filter by annotation.}
\item{variable}{Deprecated: Use /generate web service and filter by annotation.}
\item{field}{Field for which to obtain the distinct values.}
\item{somatic}{Somatic sample.}
\item{individualId}{Individual ID or UUID.}
\item{fileIds}{Comma separated list of file IDs, paths or UUIDs.}
\item{phenotypes}{Comma separated list of phenotype ids or names.}
\item{snapshot}{Snapshot value (Latest version of the entry in the specified release).}
\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{id}{Comma separated list of cohort IDs up to a maximum of 100.}
\item{name}{Comma separated list of cohort names up to a maximum of 100.}
\item{uuid}{Comma separated list of cohort IDs up to a maximum of 100.}
\item{type}{Cohort type.}
\item{creationDate}{creationDate.}
\item{modificationDate}{modificationDate.}
\item{status}{status.}
\item{internalStatus}{internalStatus.}
\item{annotation}{Cohort annotation.}
\item{acl}{acl.}
\item{samples}{Cohort sample IDs.}
\item{numSamples}{Number of samples.}
\item{release}{release.}
\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{flattenAnnotations}{Flatten the annotations?.}
\item{deleted}{Boolean to retrieve deleted cohorts.}
\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{samplesAction}{Action to be performed if the array of samples is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}
\item{annotationSetsAction}{Action to be performed if the array of annotationSets is being updated. Allowed values: \link{'ADD', 'SET', 'REMOVE'}}
\item{includeResult}{Flag indicating to include the created or updated document result in the response.}
\item{study}{Study [\link{user@}project:]study where study and project can be either the ID or UUID.}
\item{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: \link{'ADD', 'SET', 'REMOVE', 'RESET', 'REPLACE'}}
\item{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.}
}
\description{
This function implements the OpenCGA calls for managing Cohorts.
The following table summarises the available \emph{actions} for this client:\tabular{llr}{
endpointName \tab Endpoint WS \tab parameters accepted \cr
updateAcl \tab /{apiVersion}/cohorts/acl/{members}/update \tab study, members\link{*}, action\link{*}, body\link{*} \cr
aggregationStats \tab /{apiVersion}/cohorts/aggregationStats \tab study, type, creationYear, creationMonth, creationDay, creationDayOfWeek, numSamples, status, release, annotation, default, field \cr
loadAnnotationSets \tab /{apiVersion}/cohorts/annotationSets/load \tab study, variableSetId\link{*}, path\link{*}, parents, annotationSetId, body \cr
create \tab /{apiVersion}/cohorts/create \tab include, exclude, study, variableSet, variable, includeResult, body\link{*} \cr
distinct \tab /{apiVersion}/cohorts/distinct \tab study, id, name, uuid, type, creationDate, modificationDate, deleted, status, internalStatus, annotation, acl, samples, numSamples, release, field\link{*} \cr
generate \tab /{apiVersion}/cohorts/generate \tab include, exclude, study, id, somatic, individualId, fileIds, creationDate, modificationDate, internalStatus, status, phenotypes, annotation, acl, release, snapshot, includeResult, body\link{*} \cr
search \tab /{apiVersion}/cohorts/search \tab include, exclude, limit, skip, count, flattenAnnotations, study, id, name, uuid, type, creationDate, modificationDate, deleted, status, internalStatus, annotation, acl, samples, numSamples, release \cr
acl \tab /{apiVersion}/cohorts/{cohorts}/acl \tab cohorts\link{*}, study, member, silent \cr
delete \tab /{apiVersion}/cohorts/{cohorts}/delete \tab study, cohorts\link{*} \cr
info \tab /{apiVersion}/cohorts/{cohorts}/info \tab include, exclude, flattenAnnotations, cohorts\link{*}, study, deleted \cr
update \tab /{apiVersion}/cohorts/{cohorts}/update \tab include, exclude, cohorts\link{*}, study, samplesAction, annotationSetsAction, includeResult, body \cr
updateAnnotationSetsAnnotations \tab /{apiVersion}/cohorts/{cohort}/annotationSets/{annotationSet}/annotations/update \tab cohort\link{*}, study, annotationSet\link{*}, action, body \cr
}
}
\section{Endpoint /{apiVersion}/cohorts/acl/{members}/update}{
Update the set of permissions granted for the member.
}
\section{Endpoint /{apiVersion}/cohorts/aggregationStats}{
Fetch catalog cohort stats.
}
\section{Endpoint /{apiVersion}/cohorts/annotationSets/load}{
Load annotation sets from a TSV file.
}
\section{Endpoint /{apiVersion}/cohorts/create}{
Create a cohort.
}
\section{Endpoint /{apiVersion}/cohorts/distinct}{
Cohort distinct method.
}
\section{Endpoint /{apiVersion}/cohorts/generate}{
Create a cohort based on a sample query.
}
\section{Endpoint /{apiVersion}/cohorts/search}{
Search cohorts.
}
\section{Endpoint /{apiVersion}/cohorts/{cohorts}/acl}{
Return the acl of the cohort. If member is provided, it will only return the acl for the member.
}
\section{Endpoint /{apiVersion}/cohorts/{cohorts}/delete}{
Delete cohorts.
}
\section{Endpoint /{apiVersion}/cohorts/{cohorts}/info}{
Get cohort information.
}
\section{Endpoint /{apiVersion}/cohorts/{cohorts}/update}{
Update some cohort attributes.
}
\section{Endpoint /{apiVersion}/cohorts/{cohort}/annotationSets/{annotationSet}/annotations/update}{
Update annotations from an annotationSet.
}
\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
}