calcSRmat: 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: 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);

Example output

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