mafCompare {maftools} | R Documentation

## compare two cohorts (MAF).

### Description

compare two cohorts (MAF).

### Usage

    mafCompare(
      m1,
      m2,
      m1Name = NULL,
      m2Name = NULL,
      minMut = 5,
      useCNV = TRUE,
      pathways = FALSE,
      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. Default 'FALSE'
`custom_pw` | Optional. Can be a two column data.frame/tsv-file with pathway-name and genes involved in them. Default 'NULL', uses a predefined list of pathways. Applicable only when 'pathways = TRUE'
`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)

[Package maftools version 2.10.05 Index]