calcSRmat {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: fcros() and pfco().

Usage

calcSRmat(xdata, cont, test, log2.opt=0, trim.opt=0.25)

Arguments

xdata

A matrix or a table containing two biological conditions dataset to process for detecting differentially expressed genes: xdata.

cont

A vector containing the label names of the control samples: cont = c("cont01", "cont02", ...).

test

A vector containing the label names of the test samples: test = c("test01", "test02", "test03", ...).

log2.opt

A scalar equals to 0 or 1. The value 0 (default) means that data in the matrix "xdata" 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 of each gene are not used for computing its statistics "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);