qsmooth {yarn}R Documentation

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))


[Package yarn version 1.16.0 Index]