subsetGeneSet: Filter gene expression value matrix based on certain gene...

In dfjenkins3/TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

Filter gene expression value matrix based on certain gene sets.

Description

A function used to subset gene expression value matrix based on certain gene sets.

Usage

subsetGeneSet(
  theObject,
  gene_set,
  useAssay,
  obtainDiagnosis = FALSE,
  annotationColName = NULL
)

Arguments

theObject	A SummarizedExperiment object that has been pre-stored in OriginalTrainingData.RDA
gene_set	A character vector that includes gene symbols for gene signatures.
useAssay	A character string or an integer specifying the assay in the theObject that will be selected.
obtainDiagnosis	Boolean. Usually used to create training data if TRUE. Default is FALSE
annotationColName	A character string specifying the column name of disease status. Only used when creating training data. Default is NULL.

Value

A matrix with selected gene expression value if obtainDiagnosis == FALSE. If obtainDiagnosis == TRUE, return a list contains the selected gene expression value and diagnosis results for each sample.

dfjenkins3/TBSignatureProfiler documentation built on Oct. 26, 2024, 1:29 a.m.