pair.discordant.reads: Pair discordant reads

Description Usage Arguments Value Author(s)

View source: R/pair.discordant.reads.R

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

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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 Oct. 20, 2017, 12:58 a.m.