PlotTransBiasID115ToPdf: Plot transcription strand bias to a PDF file
In steverozen/ICAMSxtra: ICAMSxtra

Description Usage Arguments Value Note Examples

Plot transcription strand bias to a PDF file

1	PlotTransBiasID115ToPdf(annotated.ID.vcfs, file, pool, damaged.base = NULL)

`annotated.ID.vcfs`	ID vcfs which have been annotated with `AnnotateIDVCFsWithTransRanges`.
`file`	The name of output file.
`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.

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.

library(ICAMS)
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")
  PlotTransBiasID115ToPdf(annotated.ID.vcfs = annotated.ID.vcf,
                           file = file.path(tempdir(), "test.pdf"),
                           pool = TRUE)
}