mafCompare: compare two cohorts (MAF).

In maftools: Summarize, Analyze and Visualize MAF Files

Description

compare two cohorts (MAF).

Usage

mafCompare(m1, m2, m1Name = NULL, m2Name = NULL, minMut = 5, useCNV = TRUE)

Arguments

m1	first MAF object
m2	second MAF object
m1Name	optional name for first cohort
m2Name	optional name for second cohort
minMut	Consider only genes with minimum this number of samples mutated in atleast one of the cohort for analysis. Helful to ignore single mutated genes. Default 5.
useCNV	whether to include copy number events to compare MAFs. Only applicable when MAF is read along with copy number data. Default TRUE if available.

Details

Performs fisher test on 2x2 contigency table generated from two cohorts to find differentially mutated genes.

Value

result list

See Also

forestPlot

lollipopPlot2

Examples

primary.apl <- system.file("extdata", "APL_primary.maf.gz", package = "maftools")
relapse.apl <- system.file("extdata", "APL_relapse.maf.gz", package = "maftools")
primary.apl <- read.maf(maf = primary.apl)
relapse.apl <- read.maf(maf = relapse.apl)
pt.vs.rt <- mafCompare(m1 = primary.apl, m2 = relapse.apl, m1Name = 'Primary',
m2Name = 'Relapse', minMut = 5)

Example output

-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 45 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.265s elapsed (0.208s cpu) 
-Reading
-Validating
--Non MAF specific values in Variant_Classification column:
  ITD
-Silent variants: 19 
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.125s elapsed (0.123s cpu) 

maftools documentation built on Feb. 6, 2021, 2 a.m.