draw.DEnumber

From MetaDE v1.0.5 by Xingbin Wang

A function to plot the number of DE genes against FDR obtained from the Meta-analysis.

draw.DEnumber(result,maxcut,mlty=NULL,mcol=NULL,mlwd=NULL,mpch=NULL,FDR=TRUE) plot the number of DE genes against FDR obtained from the Meta-analysis.

Usage

draw.DEnumber(result,maxcut,mlty=NULL,mcol=NULL,mlwd=NULL,mpch=NULL,FDR=TRUE)

Arguments

result: A p-value matrix or an object file from metaDE.rawdata.pvalue,metaDE.pvalue,metaDE.minMCC, metaDE.ES
FDR: use FDR for cutpoints if true, p-value otherwise
maxcut: The maximum cut point for FDR or P-value
mlty: line type for each line. default is set
mcol: line colour. defaut is set
mlwd: line width for each line. default is set
mpch: symbol for each line. default is set

Value

A figure containing:
figurep-value(or FDR) vs numberof detected genes for individual analysis as well as meta analysis.

References

Li and Tseng (2011) and Lu, Li and Tseng (2009).

Examples

#---example 1: Meta analysis of Differentially expressed genes between two classes----------#
label1<-rep(0:1,each=5)
label2<-rep(0:1,each=5)
exp1<-cbind(matrix(rnorm(5*200),200,5),matrix(rnorm(5*200,2),200,5))
exp2<-cbind(matrix(rnorm(5*200),200,5),matrix(rnorm(5*200,1.5),200,5))
x<-list(list(exp1,label1),list(exp2,label2))

# here I used modt to generate p-values. 
DEgene<-ind.analysis(x,ind.method=rep("regt",2),tail="abs",nperm=100)

#--then you can use Fisher's method to combine the above p-values
res<-MetaDE.pvalue(DEgene,meta.method='Fisher')
draw.DEnumber(res,FDR=TRUE,maxcut=0.1)

Documentation reproduced from package MetaDE, version 1.0.5, License: GPL-2

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