preprocess: Performs normalization and/or log2 transformation

In asakellariou/git-git.bioconductor.org-packages-mAPKL: A Hybrid Feature Selection method for gene expression data

Description

This function performs normalization and/or log2 transformation on gene expression data.

Usage

    preprocess(exprsObj,log2=TRUE, norm="ALL", destname=NULL)

Arguments

exprsObj	An eSet object where its assay data will be normalized
log2	Performs logarithmic transformation of base 2 prior to any normalzation. The default value is TRUE
norm	The user may define a specific normalization method rather than "ALL" which is the default case. The available abbreviations are described in the details section
destname	Here we define the destination path and the name of the jpeg file with the density plots. The default path is the working directory

Details

The available normalization methods are:
Mean-centering normalization "mc"
z-score normalization "z"
Quantile normalization "q"
Cyclic loess normalization "cl"
Mean-centering normalization and log2 transformation "mcL2"
z-score normalization and log2 transformation "zL2"
Quantile normalization and log2 transformation "qL2"
Cyclic loess normalization and log2 transformation "clL2"

Value

rawdata	The initial gene expression values
mc.normdata	The values after 'mean-centering' normalization
z.normdata	The values after 'z-score' normalization
q.normdata	The values after 'quantile' normalization
cl.normdata	The values after 'cyclic loess' normalization
mcL2.normdata	The values after 'mean-centering' normalization and log2
zL2.normdata	The values after 'z-score' normalization and log2
qL2.normdata	The values after 'quantile' normalization and log2
clL2.normdata	The values after 'cyclic loess' normalization and log2

Author(s)

Argiris Sakellariou

Examples

library(mAPKLData)
data(mAPKLData)
varLabels(mAPKLData)
breast <- sampling(Data=mAPKLData, valPercent=40, classLabels="type", seed=135)
normTrainData <- preprocess(exprsObj=breast$trainData)

asakellariou/git-git.bioconductor.org-packages-mAPKL documentation built on June 5, 2019, 8:49 p.m.