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 1.6.0 Index]