aneuploidy.flag: Flag chromosomal aneuploidy

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

Description

Chromosomes with clear aneuploidy are detected using a simple threshold-based approach. It is used to flag chromosome with complete aneuploidy that could handicap later analysis. However it might not detect partial chromosomal aberration or aneuploidy in samples with noisy read coverage.

Usage

aneuploidy.flag(files.df, col.file = "bc.gc.gz", verbose = TRUE,
  ref.samples = NULL, centromere.pos = NULL, nb.cores = 1)

Arguments

files.df	a data.frame with information about samples such as the path to the count files.
col.file	the name of the column in 'files.df' with the path information to use. Default is 'bc.gc.gz', i.e. GC corrected bin counts.
verbose	Shoulf progress be outputted ? Default is TRUE.
ref.samples	a vector with the names of the samples to be used as reference (e.g. normals). If NULL (default) all samples are used.
centromere.pos	a vector with the position of the centromeres for each chromosome. Each position should be named with the chromosome name. If NULL (default), full chromosome aneuploidy is tested instead of arm-level deletion/duplication.
nb.cores	the number of processing cores to use, Default is 1.

Value

a data.frame with columns:

sample	the sample
chr	the chromosome
pv.loss, pv.grain	the p-value for a loss/gain
loss/gain	is the loss/gain significant
bc.norm	the normalized coverage
exp.bc	the expected normalized coverage
bc.diff	the difference between observed and expected coverage

Author(s)

Jean Monlong

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