Plot differences between APOBEC enriched and non-APOBEC enriched samples.
Plots differences between APOBEC enriched and non-APOBEC enriched samples
plotApobecDiff( tnm, maf, pVal = 0.05, title_size = 1, axis_lwd = 1, font_size = 1.2 )
tnm |
output generated by |
maf |
an |
pVal |
p-value threshold for fisher's test. Default 0.05. |
title_size |
size of title. Default 1.3 |
axis_lwd |
axis width. Default 1 |
font_size |
font size. Default 1.2 |
Plots differences between APOBEC enriched and non-APOBEC enriched samples (TCW). Plot includes differences in mutations load, tCw motif distribution and top genes altered.
list of table containing differenatially altered genes. This can be passed to forestPlot to plot results.
## Not run:
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
laml.tnm <- trinucleotideMatrix(maf = laml, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19', prefix = 'chr',
add = TRUE, useSyn = TRUE)
plotApobecDiff(laml.tnm)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.