calcSRmatMod {fcros}

Calculation of the sorted rank matrix from the dataset

Description

This is an internal function used to calculate the sorted rank matrix. It is used in the functions: fcrosMod() and pfcoMod().

Usage

calcSRmatMod(xdata, samp, log2.opt=0, trim.opt=0.25)

Arguments

xdata

A matrix containing fold changes or ratios from a biological dataset to process for searching differentially expressed genes or for detecting recurrent copy number aberrations regions: fcMat.

samp

A vector of sample label names which should appear in the columns of the matrix fcMat: samp.

log2.opt

A scalar equals to 0 or 1. The value 0 (default) means that values in the matrix "fcMat" are expressed in a log2 scale: log2.opt = 0

trim.opt

A scalar between 0 and 0.5. The value 0.25 (default) means that 25% of the lower and the upper rank values for each gene are not used for computing the statistic "ri", i.e. the interquartile range rank values are averaged: trim.opt = 0.25

Author(s)

Doulaye Dembele [e-mail]

References

Dembele D and Kaster P, Fold change rank ordering statistics: a new method for detecting differentially expressed genes, BMC bioinformatics, 2014, 15:14

Examples

#    data(fdata);