PlotTransBiasGeneExpToPdf: Plot transcription strand bias with respect to gene...
In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Description Usage Arguments Value Note Examples

Plot transcription strand bias with respect to gene expression values to a PDF file

PlotTransBiasGeneExpToPdf(
  annotated.SBS.vcf,
  file,
  expression.data,
  Ensembl.gene.ID.col,
  expression.value.col,
  num.of.bins,
  plot.type = c("C>A", "C>G", "C>T", "T>A", "T>C", "T>G"),
  damaged.base = NULL
)

`annotated.SBS.vcf`	An SBS VCF annotated by `AnnotateSBSVCF`. It must have transcript range information added.
`file`	The name of output file.
`expression.data`	A `data.table` which contains the expression values of genes. See `GeneExpressionData` for more details.
`Ensembl.gene.ID.col`	Name of column which has the Ensembl gene ID information in `expression.data`.
`expression.value.col`	Name of column which has the gene expression values in `expression.data`.
`num.of.bins`	The number of bins that will be plotted on the graph.
`plot.type`	A vector of character indicating types to be plotted. It can be one or more types from "C>A", "C>G", "C>T", "T>A", "T>C", "T>G". The default is to print all the six mutation types.
`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 p-values are calculated by logistic regression using function glm. The dependent variable is labeled "1" and "0" if the mutation from annotated.SBS.vcf falls onto the untranscribed and transcribed strand respectively. The independent variable is the binary logarithm of the gene expression value from expression.data plus one, i.e. log2 (x + 1) where x stands for gene expression value.

file <- c(system.file("extdata/Strelka-SBS-vcf/",
                      "Strelka.SBS.GRCh37.s1.vcf",
                      package = "ICAMS"))
list.of.vcfs <- ReadAndSplitStrelkaSBSVCFs(file)
SBS.vcf <- list.of.vcfs$SBS.vcfs[[1]]             
if (requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5", quietly = TRUE)) {
  annotated.SBS.vcf <- AnnotateSBSVCF(SBS.vcf, ref.genome = "hg19",
                                      trans.ranges = trans.ranges.GRCh37)
  PlotTransBiasGeneExpToPdf(annotated.SBS.vcf = annotated.SBS.vcf, 
                            expression.data = gene.expression.data.HepG2, 
                            Ensembl.gene.ID.col = "Ensembl.gene.ID", 
                            expression.value.col = "TPM", 
                            num.of.bins = 4, 
                            plot.type = c("C>A","C>G","C>T","T>A","T>C"), 
                            file = file.path(tempdir(), "test.pdf"))
}