Generate GenomicHistogram objects from BED files

Usage

genome_BED_to_histogram(
  filenames,
  n_fields = c(4, 6, 12),
  regions = NULL,
  histogram_bin_size = 1,
  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
regions: A GRanges or GRangesList object representing regions of interest defining histograms, a GRangesList object allows for the specification of non-continuous segments, default NULL - regions are taken as the set of elements with nonzero coverage
histogram_bin_size: The bin size (base-pairs) to bin signal into a histogram. Default 1
allow_overlapping_segments_per_sample: logical, if FALSE, overlapping segments in the same file will be de-duplicated in the coverage calculation, if TRUE, they will be taken as separate input, default FALSE

Value

a list of GenomicHistogram objects

Examples

if (FALSE) {
datadir <- system.file("extdata", "dna_bedfiles",  package = "HistogramZoo")
filenames <- list.files(datadir, pattern = ".bed$")
filenames <- file.path(datadir, filenames)
histograms <- genome_BED_to_histogram(
filenames = filenames,
n_fields = 6,
histogram_bin_size = 1)
}