calcSRmatMod: Calculation of the sorted rank matrix from the dataset

In fcros: A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

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);

Example output

fcros documentation built on May 31, 2019, 5:03 p.m.