Calculate mutation positions within the gene body — mutation

Given a set of mutations and gene annotation, calculate the position of each mutation within the gene body they are in.

Usage

mutation_positions(
  mutations,
  annotation,
  type = "relative",
  bin = FALSE,
  by = c(region = "gene_name"),
  threads = 1
)

Arguments

mutations: either the tibble output from find_variants. It must have columns seqnames, pos, and a third column for specifying the gene id or gene name. The mutation must be within the gene region.
annotation: Either path to the annotation file (GTF/GFF) or a GRanges object of the gene annotation.
type: character(1): the type of position to calculate. Can be one of "TSS" (distance from the transcription start site), "TES" (distance from the transcription end site), or "relative" (relative position within the gene body).
bin: logical(1): whether to bin the relative positions into 100 bins. Only applicable when type = "relative".
by: character(1): the column name in the annotation to match with the gene annotation. E.g. c("region" = "gene_name") to match the `region` column in the mutations with the `gene_name` column in the annotation.
threads: integer(1): number of threads to use.

Value

A numeric vector of positions of each mutation within the gene body. When type = "relative", the positions are normalized to the gene length, ranging from 0 (start of the gene) to 1 (end of the gene). When type = "TSS" / type = "TES", the distances from the transcription start / end site. If bin = TRUE, and type = "relative", the relative positions are binned into 100 bins along the gene body, and the output is a matrix with the number of mutations in each bin, the rows are named by the by column (e.g. gene name).

Examples

variants <- data.frame(
  seqnames = rep("chr14", 8),
  pos = c(1084, 1085, 1217, 1384, 2724, 2789, 5083, 5147),
  region = rep("Rps24", 8)
)
positions <-
 mutation_positions(
   mutations = variants,
   annotation = system.file("extdata", "rps24.gtf.gz", package = "FLAMES")
 )
#> 05:00:09 Reading annotation ...
#> 
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  |======================================================================| 100%
#>