pancanComparison {maftools} | R Documentation |
Takes MutSig results and compares them against PanCancer results.
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)
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 |
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.
ggplot object
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.
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)