subsetGeneSet {TBSignatureProfiler} | R Documentation

## 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 prestored in the RData file: OriginalTrainingData.
`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.

[Package TBSignatureProfiler version 1.6.0 Index]