coverageRegions: Plot the covered fraction of regions as a function of depth

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Plot the covered fraction of regions as a function of depth

Description

Need to first run bedtools coverage as in http://www.gettinggeneticsdone.com/2014/03/visualize-coverage-exome-targeted-ngs-bedtools.html by Stephen Turner

Usage

coverageRegions(
  path = NULL,
  pattern = NULL,
  covrg = NULL,
  plot.it = TRUE,
  xlim = NULL,
  ylim = c(0, 1),
  points.type = "l",
  plot.legend = TRUE,
  verbose = 1
)

Arguments

path	string
pattern	character string containing a regular expression passed to gsub to be removed to simplify the file basenames used in the legend (e.g. "bedtools-coverage|\.txt\.gz")
covrg	list of data frames
plot.it	logical
xlim	vector of limits for the x-axis
ylim	vector of limits for the y-axis
points.type	character indicating the type of plotting ("p"/"l"/"b")
plot.legend	logical
verbose	verbosity level (0/1)

Value

invisible list of covrg and cumcovrg

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Aug. 18, 2024, 7:43 p.m.