pair.discordant.reads: Pair discordant reads

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

Description

Compare the pair mapping between regions of the genome. The goal is to assess/detect if two distant regions are linked by more read pairs than expected (in the controls).

Usage

pair.discordant.reads(chr, start.pos, end.pos, files.df, samp, controls,
  bins.df = NULL, plot = TRUE, nb.cores = 1)

Arguments

chr	the chromosome name
start.pos	the start position
end.pos	the end position
files.df	a data.frame with the path to the bam files for each samples.
samp	the name of sample of interest.
controls	the names of the samples to use as control.
bins.df	a data.frame with the bins to use. If NULL (default), 1 Kbp bins will be used.
plot	should a graph be displayed. Default is TRUE.
nb.cores	the number of cores to use. Default is 1.

Value

a data.frame with the mapping summary for each pair of region.

Author(s)

Jean Monlong

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