maftools (version 0.99.30)

mafCompare: compare two cohorts (MAF).

Description

compare two cohorts (MAF).

Usage

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

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.

Value

result list

Details

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

See Also

forestPlot

Examples

# NOT RUN {
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)
# }