MAMA (version 2.1.0)

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 = NULL, 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 .... It is not needed when wrapper functions where used.

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 performSOGL} 5{for function topGene} 6{for function z.stat} 7{for function tspcalc} 8{for function MAP.genes}