PlotTransBiasGeneExp: 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

PlotTransBiasGeneExp(
  annotated.SBS.vcf,
  expression.data,
  Ensembl.gene.ID.col,
  expression.value.col,
  num.of.bins,
  plot.type,
  damaged.base = NULL,
  ymax = NULL
)

`annotated.SBS.vcf`	An SBS VCF annotated by `AnnotateSBSVCF`. It must have transcript range information added.
`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 character string indicating one mutation type to be plotted. It should be one of "C>A", "C>G", "C>T", "T>A", "T>C", "T>G".
`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 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)
  PlotTransBiasGeneExp(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>A")
}