medvar.norm: Median-variance normalization of bin counts

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

Description

The median and deviation to the median is normalized across samples.

Usage

medvar.norm(bc, ref.samples, bc.support = NULL, z.poisson = FALSE)

Arguments

bc	a matrix or data.frame with the bin counts (bin x sample).
ref.samples	a vector with the names of the samples to be used as reference.
bc.support	TODO
z.poisson	Should the Z-score be computed as an normal-poisson hybrid (see Details). Default is FALSE.

Value

a list with

norm.stats	a data.frame with some metrics about the normalization of each bin (row) : coverage average and standard deviation; number of outlier samples
bc.norm	a data.frame, similar to the input 'bc.df', with the normalized bin counts.

Author(s)

Jean Monlong

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