RUVcorr (version 1.4.2)

compareRanks: Compare ranking of known reference gene pairs.

Description

compareRanks allows to calculate the difference of the ranks of known reference gene pairs from two versions of the same data.

Usage

compareRanks(Y, Y.hat, ref_index, no.random = 1000, exclude_index)

Arguments

Y

A matrix of raw gene expression values.

Y.hat

A matrix of cleaned gene expression values.

ref_index

A vector of indices that are referrring to genes of interest.

no.random

An integer giving the number of random genes.

exclude_index

A vector of indices to be excluded from the selection of random genes.

Value

compareRanks returns a vector of the differences in ranks of the correlations of reference gene pairs estimated using raw or cleaned data.

Details

The correlations between all random genes and reference genes is calculated (including correlations between random and reference) using the two versions of the data. The correlations are then ranked according to their absolute value (highest to lowest). The ranks of the reference gene pairs are extracted. For a paticular reference gene pair, the difference in the ranks between the two versions of the data is calculated: Rank in Y - Rank in Y.hat

Examples

Y<-simulateGEdata(500, 500, 10, 2, 5, g=NULL,
Sigma.eps=0.1, 250, 100, intercept=FALSE, check.input=FALSE)
Y.hat<-RUVNaiveRidge(Y, center=TRUE, nu=0, kW=10)
compareRanks(Y$Y, Y.hat, ref_index=1:30, no.random=100, exclude_index=c(31:100,251:500))