qunormtrain {bapred}

Quantile normalization with “documentation by value” (Kostka & Spang, 2008)

Description

Performs quantile normalization for a covariate matrix and returns the normalized dataset together with information necessary for addon quantile normalization (Kostka & Spang, 2008) using qunormaddon.

Usage

qunormtrain(x)

Arguments

x

matrix. The covariate matrix. observations in rows, variables in columns.

Details

This function uses code from the off-CRAN package docval, version 1.0.

Value

qunormtrain returns an object of class qunormtrain. An object of class "qunormtrain" is a list containing the following components:

xnorm

matrix of quantile normalized (training) data. Observations in rows, variables in columns.

mqnts

Vector of length ncol(xnorm). Averages of sorted values, with averages taken across observations.

Author(s)

Roman Hornung

References

Kostka, D., Spang, R. (2008). Microarray based diagnosis profits from better documentation of gene expression signatures. PLoS Computational Biology 4(2):e22, <doi: 10.1371/journal.pcbi.0040022>.

Examples

data(autism)
Xtrain <- X[batch==1,]

params <- qunormtrain(x=Xtrain)

Xtrainnorm <- params$xnorm