cn.plot: Plot copy-number estimates in a region.

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Plot the copy number estimates in a genomic regions across samples.

Usage

cn.plot(files.df, gr = NULL, chr = NULL, start = NULL, end = NULL,
  samples = NULL, flanks = 10000, highlight.region = TRUE,
  draw.lines = TRUE, nb.cores = 1)

Arguments

files.df	a data.frame with the path to the different files associated with each sample.
gr	a GRange object with the region to represent. Default is NULL.
chr	the chromosome. Used if 'gr' is NULL.
start	the start position of the region. Used if 'gr' is NULL.
end	the end position of the region. Used if 'gr' is NULL.
samples	the set of samples to represent.
flanks	the size of the flanking region. Default is 10000.
highlight.region	Should the input region highlighted. Default is TRUE.
draw.lines	Should lines be drawn to represent each sample. Default is TRUE.
nb.cores	number of cores to use. Default is 1. Increase number if many samples are to be used.

Value

a ggplot object

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.