draw.DEnumber

0th

Percentile

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).

See Also

count.DEnumber

Aliases
  • draw.DEnumber
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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