normalizeTissueAware {yarn} | R Documentation

## Normalize in a tissue aware context

### Description

This function provides a wrapper to various normalization methods developed. Currently it only wraps qsmooth and quantile normalization returning a log-transformed normalized matrix. qsmooth is a normalization approach that normalizes samples in a condition aware manner.

### Usage

    normalizeTissueAware(obj, groups, normalizationMethod = c("qsmooth",
      "quantile"), ...)

### Arguments

`obj` | ExpressionSet object
`groups` | Vector of labels for each sample or a column name of the phenoData slot for the ids to filter. Default is the column names
`normalizationMethod` | Choice of 'qsmooth' or 'quantile'
`...` | Options for `qsmooth` function or `normalizeQuantiles`

### Value

ExpressionSet object with an assayData called normalizedMatrix

### Source

The function qsmooth comes from the qsmooth packages currently available on github under user 'kokrah'.

### Examples

    data(skin)
    normalizeTissueAware(skin,"SMTSD")

[Package yarn version 1.16.0 Index]