clinicalEnrichment {maftools} | R Documentation

## Performs mutational enrichment analysis for a given clinical feature.

### Description

Performs paiwise and groupwise fisher exact tests to find differentially enriched genes for every factor within a clinical feature.

### Usage

    clinicalEnrichment(
      maf,
      clinicalFeature = NULL,
      annotationDat = NULL,
      minMut = 5,
      useCNV = TRUE
    )

### Arguments

`maf` | `MAF` object
`clinicalFeature` | columns names from 'clinical.data' slot of `MAF` to be analysed for.
`annotationDat` | If MAF file was read without clinical data, provide a custom `data.frame` or a tsv file with a column containing Tumor_Sample_Barcodes along with clinical features. Default NULL.
`minMut` | Consider only genes with minimum this number of samples mutated. Default 5.
`useCNV` | whether to include copy number events. Only applicable when MAF is read along with copy number data. Default TRUE if available.

### Value

result list containing p-values

### See Also

`plotEnrichmentResults`

### Examples

    ## Not run:
    laml.maf = system.file('extdata', 'tcga_laml.maf.gz', package = 'maftools')
    laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools')
    laml = read.maf(maf = laml.maf, clinicalData = laml.clin)
    clinicalEnrichment(laml, 'FAB_classification')

    ## End(Not run)

[Package maftools version 2.2.10 Index]