Generates an S3 GenomicHistogram object

Generates an S3 GenomicHistogram object

Usage

GenomicHistogram(
  histogram_data = double(),
  interval_start = integer(),
  interval_end = integer(),
  region_id = character(),
  bin_width = integer(),
  chr = character(),
  strand = c("*", "+", "-"),
  intron_start = integer(),
  intron_end = integer(),
  consecutive_start = integer(),
  consecutive_end = integer()
)

Arguments

histogram_data

vector of counts/density

interval_start

integer vector representing the starts of intervals

interval_end

integer vector representing the ends of intervals

region_id

character identifier for the region of interest

bin_width

integer width of histogram bins, if missing, estimated from interval_start and interval_end

chr

chromosome name

strand

strand

intron_start

integer vector representing the starts of introns (optional: to represent intron-spanning histograms on transcripts)

intron_end

integer vector representing the ends of introns (optional: to represent intron-spanning histograms on transcripts)

consecutive_start

start of intervals, integer vector representing an intronless set of bins - defaults to starting at 1

consecutive_end

end of intervals, integer vector representing an intronless set of bins - defaults to starting at bin_width

Value

a GenomicHistogram object

Examples

x = GenomicHistogram(
histogram_data = runif(10),
interval_start = 1:10,
interval_end = 1:10,
chr = "chr1",
strand = "+")