IDD.IRR: Integration-driven Discovery and Integration-driven Revision...

In metaRNASeq: Meta-Analysis of RNA-Seq Data

Description

Calculates the gain or the loss of differentially expressed genes due to meta-analysis compared to individual studies.

Usage

IDD.IRR(meta_de, ind_de)

Arguments

meta_de	Vector of differentially expressed tags (or indices of these tags) with the meta-analysis
ind_de	List of vectors storing differentially expressed tags (or indices of these tags) in each individual study

Value

DE	Number of Differentially Expressed (DE) genes
IDD	Integration Driven Discoveries: number of genes that are declared DE in the meta-analysis that were not identified in any of the individual studies alone.
Loss	Number of genes that are declared DE in individual studies but not in meta-analysis.
IDR	Integration-driven Discovery Rate: proportion of genes that are identified as DE in the meta-analysis that were not identified in any of the individual studies alone.
IRR	Integration-driven Revision Rate: percentage of genes that are declared DE in individual studies but not in meta-analysis.

Author(s)

Guillemette Marot

References

Marot, G., Foulley, J.-L., Mayer, C.-D., Jaffrezic, F. (2009) Moderated effect size and p-value combinations for microarray meta-analyses. Bioinformatics. 25 (20): 2692-2699.

Examples

data(rawpval)
adjpval<-lapply(rawpval, FUN=function(x) p.adjust(x, method="BH"))
ind_smalladjp<-lapply(adjpval, FUN=function(x) which(x <= 0.05))
#indicators corresponding to the inverse normal p-value combination
invnormcomb <- invnorm(rawpval,nrep=c(8,8), BHth = 0.05) 
IDD.IRR(invnormcomb$DEindices,ind_smalladjp)
#indicators corresponding to the p-value combination with Fisher's method
fishcomb <- fishercomb(rawpval, BHth = 0.05)
IDD.IRR(fishcomb$DEindices,ind_smalladjp)

Example output

     DE     IDD    Loss     IDR     IRR 
1321.00   25.00   79.00    1.89    5.75 
     DE     IDD    Loss     IDR     IRR 
1343.00   15.00   47.00    1.12    3.42 

metaRNASeq documentation built on Oct. 1, 2021, 5:07 p.m.