normalizeTissueAware: Normalize in a tissue aware context

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

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")

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