clinicalEnrichment: Performs mutational enrichment analysis for a given clinical...

In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

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)

PoisonAlien/maftools documentation built on April 7, 2024, 2:49 a.m.