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,
  normSampleSize = FALSE, file = NULL, width = 6, height = 6,
  pointSize = 3, labelSize = 3)

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.

normSampleSize

normalizes gene sizes to draw bubble plot. Requires inputSampleSize. i.e, bubble sizes proportional to fraction of samples in which the gene is mutated.

file

basename for output file (both raw data and plot are saved)

width

width of the file to be saved.

height

height of the file to be saved.

pointSize

size for scatter plot. Default 1.

labelSize

label text size. Default 3

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

ggplot object

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, normSampleSize = TRUE)

[Package maftools version 1.8.0 Index]