maftools: clinicalEnrichment – R documentation

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clinicalEnrichment

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
)

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.

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

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)

maftools

Summarize, Analyze and Visualize MAF Files

v2.6.05

MIT + file LICENSE

Authors

Anand Mayakonda [aut, cre] (<https://orcid.org/0000-0003-1162-687X>)

Initial release

2015-12-14