Last data update: 2014.03.03
|
R: Plots for Meta-analysis of gene expression data.
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.
Results
|