CountPlot: Plots for Meta-analysis of gene expression data.

In Bioconductor/GeneMeta: MetaAnalysis for High Throughput Experiments

Plots for Meta-analysis of gene expression data.

Description

Plots for meta-analysis

Usage

IDRplot(m,CombineExp=1:(length(grep("zSco_Ex",colnames(m)))),colPos="black",colNeg="red",pchPos="*",pchNeg="*",type="b",ylab="IDR",xlab="z threshold",...)
CountPlot(kkk,cols,Score=c("FDR","zSco"),kindof=c("two.sided","pos","neg"),type="b",pch="*",ylab="Number of genes",xlab="FDR threshold",CombineExp=1:((ncol(m)-6)/2-1) ,...)

Arguments

m	result matrix of the function zScores
type	plot parameter
ylab	plot parameter
xlab	plot parameter
pch	plot parameter
colPos	color for positive z scores
colNeg	color for negative z scores
pchPos	symbol for positive z scores
pchNeg	symbol for negative z scores
CombineExp	vector of integer- which experiments should be combined-default:all experiments
kkk	result object of function zScoreFDR
cols	vector of cols, one for each experiment, and one for the combination
Score	should the FDR or the zScore be plotted
kindof	"pos", "neg" or "two.sided"
...	additional plot parameter

Details

IDRplot produces a plot described in Choi et al.

Author(s)

M.Ruschhaupt

References

Choi et al, Combining multiple microarray studies and modeling interstudy variation. Bioinformatics, 2003, i84-i90.

Bioconductor/GeneMeta documentation built on Nov. 2, 2024, 6:35 a.m.