Generate GenomicHistogram objects from BED files using coordinates defined by a GTF file

Generate GenomicHistogram objects from BED files using coordinates defined by a GTF file

Usage

transcript_BED_to_histogram(
  filenames,
  n_fields = c(4, 6, 12),
  gtf,
  histogram_bin_size = 1,
  gene_or_transcript = c("gene", "transcript"),
  select_strand = c("*", "+", "-"),
  select_chrs = NULL,
  select_ids = NULL,
  allow_overlapping_segments_per_sample = F
)

Arguments

filenames

A vector of BED filenames. The name column of the BED files must indicate gene or transcript name

n_fields

Number of columns in the BED file that conform to BED file standards, default 4

gtf

A GTF file

histogram_bin_size

The bin size (base-pairs) to bin signal into a histogram, default 1

gene_or_transcript

gene or transcript indicating whether histograms should be built on gene coordinates or transcript coordinates, default gene

select_strand

*, + or - to filter regions by strand, default '*'

select_chrs

a vector of chromosomes to filter regions by chromosome, default NULL

select_ids

gene or transcript ids to filter regions by gene or transcript name, must correspond to GTF ids, default NULL

allow_overlapping_segments_per_sample

logical, if FALSE, overlapping segments in the same region in the same file will be de-duplicated in the coverage calculation, default NULL NOTE: regions are determined by GTF gene/transcript IDs and the name column of BED files. If TRUE, they will be taken as separate input, default FALSE

Value

a list of GenomicHistogram objects

Examples

if (FALSE) {
datadir <- system.file("extdata", "rna_bedfiles", package = "HistogramZoo")
filenames <- file.path(datadir, paste0("Sample.", 1:20, ".bed"))
gtf <- system.file("extdata", "genes.gtf", package = "HistogramZoo")

histograms <- transcript_BED_to_histogram(
filenames = filenames,
n_fields = 12,
gtf = gtf,
gene_or_transcript = "gene",
histogram_bin_size = 10)
}