Description Usage Arguments Details Value See Also Examples
View source: R/plotApobecDiff.R
Plots differences between APOBEC enriched and non-APOBEC enriched samples
1 2 3 4 5 6 7 8 | 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.
trinucleotideMatrix
plotSignatures
1 2 3 4 5 6 7 8 | ## 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)
|
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