qsmooth: Quantile shrinkage normalization

In QuackenbushLab/yarn: YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Quantile shrinkage normalization

Description

This function was modified from github user kokrah.

Usage

qsmooth(obj, groups, norm.factors = NULL, plot = FALSE, window = 0.05,
  log = TRUE)

Arguments

obj	for counts use log2(raw counts + 1)), for MA use log2(raw intensities)
groups	groups to which samples belong (character vector)
norm.factors	scaling normalization factors
plot	plot weights? (default=FALSE)
window	window size for running median (a fraction of the number of rows of exprs)
log	Whether or not the data should be log transformed before normalization, TRUE = YES.

Value

Normalized expression

Source

Kwame Okrah's qsmooth R package

Examples

data(skin)
head(yarn:::qsmooth(skin,groups=pData(skin)$SMTSD))

QuackenbushLab/yarn documentation built on March 7, 2024, 3:53 p.m.