bic.quantile.normalize.htseq.counts: Use quantile normalization to normalize raw HTSeq counts

In bic-mskcc/bicrnaseq: MSKCC Bioinformatics Core RNASeq

Description

Run normalizeBetweenArrays() function to normalize raw HTSeq counts and return a list containing both raw and normalized counts

Usage

bic.quantile.normalize.htseq.counts(htseq.counts, key = NULL)

Arguments

htseq.counts	matrix containing raw counts from HTSeq. One column per sample, one row per gene
key	matrix where column one contains sample IDs that matches those in counts file, and column two contains the condition groups to which they belong. Only those samples that are in the key matrix will be included in the normalization

Value

list containing two matrices (one of raw counts and one of quantile normalized counts) and a vector of gene symbols if one was included in the raw counts matrix

bic-mskcc/bicrnaseq documentation built on May 24, 2019, 3:04 a.m.