normalizecounts: Normalize a list of count matrices

In lamortenera/epicseg: Chromatin Segmentation in R

Description

Given a list of count matrices, corresponding rows across the different count matrices are made comparable with a normalization procedure. Rows correspond if they have the same row name in all count matrices.

Usage

normalizecounts(clist, normFun = quantileNormalization, nthreads = 1, ...)

Arguments

clist	A list of count matrices. Each matrix must have the same set of row names and the same number of columns.
normFun	A normalization function to use. Such a function takes a matrix as input argument and returns a matrix with the same dimensions as output. The goal of this function is to make the columns comparable. The functions quantileNormalization and linearNormalization are two already implemented, customizable functions.
nthreads	The maximum number of threads. Parallelization is done on the histone marks using mclapply. If also normFun accepts the nthreads argument, parallelization will be nested, with the outer level using min(nthreads, nmarks) threads, and the inner level using floor(nthreads/nthreadsOuter) threads.
...	options passed to normFun.

Value

A list of count matrices similar to the input list, but with the rows of each matrix normalized.

lamortenera/epicseg documentation built on May 20, 2019, 7:34 p.m.