rnaSeqNormalizer.gtex: Define an object of class rnaSeqNormalizer from a GTEx matrix

In PriceLab/rnaSeqNormalization: rnaSeqNormalizer: Cory Funk's favorite methods

Description

Cory, Michael and Max brewed up their preferred method, to which I have added asinh and vst (variance stabilizing normalization), here packaged up for easy reuse. ensg identifers are mapped to geneSymbols. duplicated geneSymbols are eliminated in favor of the one with the highest score according to the selected statistic: mean, median, sd (standard deviation)

Usage

rnaSeqNormalizer.gtex(x, algorithm, duplicate.selection.statistic)

Arguments

x	a matix or data.frame of RNA-seq counts, rows are genes, columnns are mostly samples
algorithm	a character string, one of "log+scale", "asinh", "vsn
duplicate.selection.statistc	a character string, one of "median", "mean", "sd". when duplicate geneSymbols are supplied or obtained from name mapping, the highest scoring of the duplicates, by the specified meansure, is kept; all others are dropped

Value

A normalized matrix with dimensions, row and column names preserved

PriceLab/rnaSeqNormalization documentation built on Jan. 23, 2020, 4:48 a.m.