intCor: Correlation of Correlations
In MergeMaid: Merge Maid

Description Usage Arguments Details Value See Also Examples

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

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

`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

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.

The output is an object of class mergeCor.

mergeCor-class,intcorDens

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")
 }