mafCompare: compare two cohorts (MAF).

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

compare two cohorts (MAF).

Description

compare two cohorts (MAF).

Usage

mafCompare(
  m1,
  m2,
  m1Name = NULL,
  m2Name = NULL,
  minMut = 5,
  useCNV = TRUE,
  pathways = NULL,
  custom_pw = NULL,
  pseudoCount = FALSE
)

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. Default TRUE if available.. Not applicable when 'pathways = TRUE'
pathways	Summarize genes by pathways before comparing. Can be either 'sigpw' or 'smgbp', 'sigpw' uses known oncogenic signalling pathways (Sanchez/Vega et al) whereas 'smgbp' uses pan cancer significantly mutated genes classified according to biological process (Bailey et al). Default NULL
custom_pw	Optional. Can be a two column data.frame/tsv-file with pathway-name and genes involved in them. Default 'NULL'. This argument is mutually exclusive with pathdb
pseudoCount	If TRUE, adds 1 to the contingency table with 0's to avoid 'Inf' values in the estimated odds-ratio.

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)

PoisonAlien/maftools documentation built on Nov. 10, 2024, 6:01 p.m.