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

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

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)

thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.