quant.norm: Quantile normalization

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

Description

Quantile normalization of the bin counts. After such normalization, each sample has exactly the same global bin count distribution.

Usage

quant.norm(bc.df, nb.cores = 1, norm.stats.comp = TRUE)

Arguments

bc.df	a data.frame with 'chr', 'start', 'end' columns and then one column per sample with its bin counts.
nb.cores	the number of cores to use. Default is 1.
norm.stats.comp	Should some statistics on the normalized bin count be computed (mean, sd, outliers). Default is TRUE.

Value

a list with

norm.stats	a data.frame witht 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.