PlotTransBiasID115: Plot transcription strand bias
In steverozen/ICAMSxtra: ICAMSxtra

Description Usage Arguments Value Note Examples

Plot transcription strand bias

1	PlotTransBiasID115(annotated.ID.vcf, pool, damaged.base = NULL, ymax = NULL)

`annotated.ID.vcf`	An ID VCF annotated by `AnnotateIDVCFsWithTransRanges`. It must have transcript range information added.
`pool`	if true, 36 categories will be pooled to 4 categories by removing trinucleotide context. This can be done if the counts of individual categories are too low, to increase power.
`damaged.base`	One of `NULL`, `"purine"` or `"pyrimidine"`. This function allocates approximately equal numbers of mutations from `damaged.base` into each of `num.of.bins` bin by expression level. E.g. if `damaged.base` is `"purine"`, then mutations from A and G will be allocated in approximately equal numbers to each expression-level bin. The rationale for the name `damaged.base` is that the direction of strand bias is a result of whether the damage occurs on a purine or pyrimidine. If `NULL`, the function attempts to infer the `damaged.base` based on mutation counts.
`ymax`	Limit for the y axis. If not specified, it defaults to NULL and the y axis limit equals 1.5 times of the maximum mutation counts in a specific mutation type.

A list whose first element is a logic value indicating whether the plot is successful. The second element is a named numeric vector containing the p-values printed on the plot.

The strand bias statistics are Benjamini-Hochberg q-values based on two-sided binomial tests of the mutation counts on the transcribed and untranscribed strands relative to the actual abundances of C and T on the transcribed strand. On the plot, asterisks indicate q-values as follows *, Q<0.05; **, Q<0.01; ***, Q<0.001.

file <- c(system.file("extdata/Strelka-ID-vcf/",
                      "Strelka.ID.GRCh37.s1.vcf",
                      package = "ICAMSxtra"))
ID.vcf <- ICAMS::ReadAndSplitVCFs(file, variant.caller = "strelka")$ID
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  annotated.ID.vcf <- AnnotateIDVCFsWithTransRanges(ID.vcf, ref.genome = "hg19",
                                                    trans.ranges = ICAMS::trans.ranges.GRCh37,
                                                    vcf.names = "Strelka.ID.GRCh37.s1.vcf")
  #' alternatively run below code to skip call to AnnotateIDVCFsWithTransRanges 
  #' load(c(system.file("extdata/annotated.ID.vcf.rda",package = "ICAMSxtra")))
  PlotTransBiasID115(annotated.ID.vcf = annotated.ID.vcf[[1]],
                      pool = TRUE)
}