clinicalEnrichment {maftools} | R Documentation

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

### Description

Performs pairwise 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,
      pathways = FALSE
    )

### 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 if available. Default TRUE. Not applicable when 'pathways = TRUE'
`pathways` | Summarize genes by pathways before comparing. Default 'FALSE'

### Details

Performs fishers test on 2x2 contingency table for WT/Mutants in group of interest vs rest of the sample. Odds Ratio indicate the odds of observing mutant in the group of interest compared to wild-type

### 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 2.10.05 Index]