Normalize in a tissue aware context

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"),
  ...
)

Source

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

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

Examples

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