PlotTransBiasGeneExp: Plot transcription strand bias with respect to gene...

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Plot transcription strand bias with respect to gene expression values

Description

Plot transcription strand bias with respect to gene expression values

Usage

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

Arguments

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.

Value

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.

Note

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. log_2 (x + 1) where x stands for gene expression value.

Examples

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")
}

ICAMS documentation built on June 22, 2024, 6:47 p.m.