ds.addPhenoData2eSet: Add Phenotype data to ExpressionSet

In isglobal-brge/dsOmicsClient: DataSHIELD client site Omics association functions.

Add Phenotype data to ExpressionSet

Description

Add new phenotype data contained on a data.frame to an ExpressionSet. The ExpressionSet may or may not already have phenotype data. If the data.frame contains a phenotype already present on the ExpressionSet, the server function will throw an exception. The pehnotypes data.frame has to contain an ID column which does not need to contain exactly the same individuals as the ExpressionSet, only the matching individuals will be updated, no new individuals will be introduced or removed from the ExpressionSet

Usage

ds.addPhenoData2eSet(
  x,
  pheno,
  identifier = "ID",
  alternate_eset_id = NULL,
  newobj.name = NULL,
  complete_cases = TRUE,
  datasources = NULL
)

Arguments

x	character Name of the ExpressionSet on the study server
pheno	character Name of the data.frame with the new phenotypes on the study server
identifier	character (default "ID") Name of the ID column on the phenotypes data.frame
alternate_eset_id	character (default NULL) Alternate ID of the eSet pheno data, by default the rownames of the eSet pheno data act as ID, use this argument if the ID to merge the individuals is on a column of the pheno data. Input NULL for the standard behaviour of using the rownames of the pheno data as ID.
newobj.name	character (default NULL) If NULL, the original ExpressionSet will be overwritten, otherwise the new ExpressionSet will be assigned to a variable named after this argument
complete_cases	bool (default TRUE) If TRUE only the matching individuals between the ExpressionSet and the phenotypes table will be included on the resulting ExpressionSet. If FALSE all the individuals on the input ExpressionSet will be on the output ExpressionSet
datasources	a list of DSConnection-class (default NULL) objects obtained after login

Value

This function does not have an output. It creates an eSet object on the study server.

isglobal-brge/dsOmicsClient documentation built on March 20, 2023, 3:52 p.m.