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

In MAMA: Meta-Analysis of MicroArray

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

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

Value

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

Author(s)

Ivana Ihnatova

MAMA documentation built on Jan. 15, 2017, 3:05 p.m.