count.DEnumber: Count the number of differentially expressed (DE) genes

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/utility03282012.r

Description

a function to summary the number of DE genes at given p-value or FDR thresholds.

Usage

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count.DEnumber(result, p.cut, q.cut)

Arguments

result

A p-value matrix or an object file from metaDE.pvalue,metaDE.minMCC, metaDE.ES

p.cut

a numeric vecter to specify the p-value thresholds at which the DE number is counted.

q.cut

a numeric vecter to specify the FDR thresholds at which the DE number is counted.

Details

To count the DE number at FDR thresholds, the p-values were corrected by Benjamini-Hochberg procedure.

Value

a list with components:

pval.table

a table contains the DE numbers counted at given p-value thresholds.

FDR.table

a table contains the DE numbers counted at given FDR thresholds.

Author(s)

Jia Li and Xingbin Wang

References

Benjamini Y, Hochberg Y: Controlling the False Discovery Rate - a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B-Methodological 1995, 57(1):289-300.

See Also

draw.DEnumber

Examples

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#---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)
count.DEnumber(res,p.cut=c(0.01,0.05),q.cut=c(0.01,0.05))

MetaDE documentation built on May 29, 2017, 9 a.m.