overlap_score_summary_vs_bin_size: Calculate and Summarize TopDom Overlap Scores as Function of...

In HenrikBengtsson/TopDomStudy: TopDom Study by Segal et al.

Description

Calculate and Summarize TopDom Overlap Scores as Function of Bin Size

Usage

overlap_score_summary_vs_bin_size(
  dataset,
  chromosomes,
  bin_sizes,
  rhos,
  reference_rhos = rep(1/2, times = length(rhos)),
  window_size = 5L,
  nsamples = 50L,
  weights = c("by_length", "uniform"),
  domain_length = NULL,
  fig_path = "figures",
  fig_format = c("png", "pdf"),
  xlim = NULL,
  ylim_score = c(0, 1),
  verbose = FALSE
)

Arguments

dataset	(character string) The name of the data set.
chromosomes	(character vector) Chromosomes to process.
bin_sizes	(numeric vector) The set of bin sizes (in bps) to process.
rhos	(numeric vector) The set of fractions (in (0,0.5]) to process.
reference_rhos	(numeric vector) The set of fractions (in (0,0.5]) to process.
window_size	(integer) The TopDom windows size. Argument passed as window.size to TopDom::TopDom().
nsamples	(integer) Number of random samples for produce.
weights	(character string) A character string specifying how overlap scores across domains should be weighted. Argument passed as is to overlap_score_summary().
domain_length	(optional; character string or numeric vector of length two) If specified, controls how to filter out too short or too long TopDom domains. Argument passed as is to overlap_score_summary().
fig_path	If non-NULL, an image file is written to this path.
fig_format	Image format used for image files.
xlim	The range on the x axis.
ylim_score	The range of overlap scores on the y axis.
verbose	(logical) If TRUE, verbose output is produced.

Details

Image files are written to the ‘figures/’ folder (created if missing).

Value

A three-dimensional character array of pathname names where the first dimension specify chromosomes, the second bin_sizes, and the third 'rhos'.

See Also

Internal, overlap_score_summary_grid() is used to calculate overlap scores over (chromosome, bin_size, rho).

HenrikBengtsson/TopDomStudy documentation built on May 14, 2021, 1:49 p.m.