plotgene: Function to visuaze change in expression of one gene

In MAMA: Meta-Analysis of MicroArray

Description

Various methods for meta-analysis provide different outputs. Function takes an output from function metagene as input and draws a plot.

Usage

plotgene(gene, datalabels=NULL, type, col=c("green", "red"),cex=c(0.7),sig=0.05)

Arguments

gene	A list, output from function metagene
datalabels	A character vector, names of the data sets and for meta-analysis results. If NULL, dummy names Study1, Study2, Study3, ..., Meta are created.
type	A numeric vector indicating which function the slots of gene come from. It it is not necessary, if the slots come from the results of the wrapper functions.
col	colors for unsignificant/significant
cex	Font size for labels in unsignificant/significant part of the chart
sig	Significance threshold for p-values graph

Details

Function plotgene2 is based on traditional graphics, wheras function plotgene on grid.

For type please use:

• 0 for functions: pvalcombination, pvalcombination.paired, EScombination or EScombination.paired, metaMA

• 1 for function ES.GeneMeta

• 2 for function zScores

• 3 for function ScoresFDR

• 4 for function performSOGL

• 5 for function topGene or RankProduct

• 6 for function posterior.mean

• 7 for function MAP.genes or MAP.Matches

• 8 for function MC

• 9 for function compute.RQ

• 10 for function METRADISC

Author(s)

Ivana Ihnatova

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