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MAMA (version 2.2.1)

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. It can be NULL if the wrapper functions were used for the analysis.
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.
  • 1for functions: pvalcombination, pvalcombination.paired, EScombination or EScombination.paired
  • 2for function zScores
  • 3for function ScoresFDR
  • 4for function performSOGL
  • 5for function topGene
  • 6for function z.stat
  • 7for function MAP.genes