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

Description Usage Arguments Value Author(s)

View source: R/cn.plot.R

Description

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

Usage

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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 July 1, 2018, 10:14 p.m.