coverage.plot: Plot the bin coverage in a region

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

Description

Plot the bin coverage in a genomic regions across samples. The files ('bc.f', 'norm.stats.f') must be ordered and indexed.

Usage

coverage.plot(chr, start, end, bc.f, norm.stats.f = NULL, sv.df = NULL,
  ref.samples = NULL, boxplot = FALSE, samples = NULL, files.df = NULL,
  anno.df = NULL, anno.col = "geneName", flanks = 10000,
  absolute.position = TRUE, nb.cores = 1)

Arguments

chr	the chromosome
start	the start position of the region
end	the end position of the region
bc.f	the path to the bin count file.
norm.stats.f	the path to the normalization statistics file.
sv.df	the data.frame with the calls.
ref.samples	the names of the reference samples.
boxplot	should the reference be represented as boxplots. If FALSE, violin plots will be used.
samples	the set of samples to represent.
files.df	a data.frame with the path to the different files associated with each sample. If 'sample' is absent from 'bc.f' the correct file from 'files.df' will be used. Default is NULL.
anno.df	a data.frame with additional information (e.g. gene annotation) to be added to the graph.
anno.col	the name of 'anno.df' column to use to differentiate elements in the graph. E.g. 'geneName' to color the genes in the graph.
flanks	the size of the flanking region. Default is 10000.
absolute.position	should the bins be placed in absolute position. Default is TRUE. If FALSE, distant bins might be displayed next to each other if no bins are available in between (useful for targeted sequencing).
nb.cores	the number of cores to use. Default is 1.

Value

a ggplot object

Author(s)

Jean Monlong

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