compare two cohorts (MAF).
compare two cohorts (MAF).
mafCompare(m1, m2, m1Name = NULL, m2Name = NULL, minMut = 5, useCNV = TRUE)
m1 |
first |
m2 |
second |
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. |
Performs fisher test on 2x2 contigency table generated from two cohorts to find differentially mutated genes.
result list
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.