pancanComparison {maftools} | R Documentation

## Perform PacCancer analysis

### Description

Takes MutSig results and compares them against PanCancer results.

### Usage

    pancanComparison(
      mutsigResults,
      qval = 0.1,
      cohortName = "input",
      inputSampleSize = NULL,
      label = 1,
      genesToLabel = NULL,
      pointSize = 0.1,
      labelSize = 0.8
    )

### Arguments

`mutsigResults` | MutSig results (usually sig_genes.txt). Can be gz compressed.
`qval` | qvalue threshold to define SMG. Default 0.1
`cohortName` | Input cohort name.
`inputSampleSize` | Sample size from MAF file used to generate mutSig results. Optional.
`label` | Default 1. Can be 1, 2 or 3.
`genesToLabel` | Default NULL. Exclusive with label argument.
`pointSize` | size for scatter plot. Default 1.
`labelSize` | label text size. Default 1

### Details

This function takes MutSig results and compares them against panCancer cohort (~5000 tumor samples from 21 cancer types). This analysis can reveal novel genes exclusively mutated in input cohort.

### Value

result table

### References

Lawrence MS, Stojanov P, Mermel CH, et al. Discovery and saturation analysis of cancer genes across 21 tumor types. Nature. 2014;505(7484):495-501. doi:10.1038/nature12912.

### Examples

    laml.mutsig <- system.file("extdata", "LAML_sig_genes.txt.gz", package = "maftools")
    pancanComparison(mutsigResults = laml.mutsig, qval = 0.1, cohortName = 'LAML', inputSampleSize = 200, label = 1)

[Package maftools version 2.3.30 Index]