MergeMaid (version 2.44.0)

intCor: Correlation of Correlations

Description

Given a mergeExpressionSet, this function calculates the study specific correlation matrices, and, for each gene, the correlation of correlations.

Usage

intCor(x,method= c("pearson", "spearman"),exact,...)

Arguments

x

Object of class mergeExpressionSet.

method

Method used to calculate correlation coefficient. If exact is TRUE, the available methods to use is "spearman" and "pearson"; If exact is FALSE, the available methods to use is "pearson".

exact

If exact is TRUE, we use the standard method the calculate the integrative correlation; If exact is FALSE, we use the approximate method the calculate.

...

Not implemented at this time

Value

Details

Integrative correlation coefficients are calcualted as follows. The first step is to identify the n genes common to all studies. Within each study, we calculate the correlation coefficient between gene g, and every other common gene. This gives a vector of length n-1. For a pair of studies, S1 and S2, we calculate the correlation of correlations for gene g. When there are more than 2 studies under consideration, all pairwise correlation of correlations are calculated and averaged.

See Also

mergeCor-class,intcorDens

Examples

if(require(Biobase) & require(MASS)){
  data(mergeData)
  merged  <-mergeExprs(sample1,sample2,sample3)
  corcor  <-intCor(merged,method="spearman")
  
  plot(merged)
  hist(corcor)

  corcor  <-intCor(merged,method="pearson",exact=FALSE)
  corcor  <-intCor(merged[1:2])
  corcor  <-intCor(merged,exact=TRUE)

  vv<-c(1,3)
  corcor1  <-intCor(merged[vv])
  plot(merged,xlab="study A",ylab="study B",main="CORRELATION OF CORRELATION",col=3,pch=4)
  hist(corcor1,xlab="CORRELATION OF CORRELATION")
 }