MAMA (version 1.0.2)

join.DEG: Function to join vectors of differentially expressed genes to one list

Description

The function takes outputs from meta-analysis of microarrays, extracts names of differentially expressed genes from them and joins these names into one list, where each slot refer to one output.

Usage

join.DEG(..., genenames, type, cutoff)

Arguments

...

Outputs from different function for methods of meta-analysis of microarray

genenames

a character vector - names of all genes (or probe ID) included in meta-analysis = rownames of gene expression data matrix

type

a numeric vector idicating from which function the output is, kth element in type corresponds to kth element of ...

cutoff

a numeric value - a cutoff level for p-value to select significant genes

Value

• A list in which each slot refers to one meta-analytical method and contains names of differentially expressed genes found by the method.

Details

Values below have to be used in type.

• 1

{for functions: pvalcombination, pvalcombination.paired, EScombination or EScombination.paired} 2{for function zScores} 3{for function ScoresFDR} 4{for function OrderedList} 5{for function topGene} 6{for function z.stat} 7{for function tspcalc} 8{for function MAP.genes}

Examples

## The function is currently defined as
function(...,genenames, type, cutoff)
{ 
args<-list(...)
N<-length(args)
if (N!=length(type)) stop ("Vector type has not correct lenght")
genelist<-list()

for (i in 1:N)
{
if (type[i]==1) {genelist[[i]]<-genenames[args[[i]]$Meta]}
if (type[i]==2) {}
if (type[i]==3) {genelist[[i]]<-rownames(args[[i]]$two.sided)[args[[i]]$two.sided[,
 8]<cutoff]}
if (type[i]==4) {genelist[[i]]<-args[[i]]$intersect}
if (type[i]==5) {genelist[[i]]<-unique(c(rownames(args[[i]]$Table1),rownames(
 args[[i]]$Table2)))}
if (type[i]==6) {genelist[[i]]<-rownames(args[[i]])[args[[i]]$Pvalue<cutoff]}
if (type[i]==7) {genelist[[i]]<-genenames[args[[i]]$index]}
if (type[i]==8) {genelist[[i]]<-unique(unlist(args[[i]]))}
  }
return(genelist)
  }