Filter gene expression value matrix based on certain gene sets.

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.