getSignificantGenes {stageR} | R Documentation |
This functions returns a matrix with significant genes by aggregated testing of its respective transcripts.
getSignificantGenes(object, ...) ## S4 method for signature 'stageRTx' getSignificantGenes(object)
object |
an object of the |
A matrix with significant genes and their corresponding FDR-adjusted screening stage (aggregated) p-value.
Van den Berge K., Soneson C., Robinson M.D., Clement L. (2017). stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biology 18:151. https://doi.org/10.1186/s13059-017-1277-0
#make identifiers linking transcripts to genes set.seed(1) genes=paste0("gene",sample(1:200,1000,replace=TRUE)) nGenes=length(table(genes)) transcripts=paste0("tx",1:1000) tx2gene=data.frame(transcripts,genes) #gene-wise q-values pScreen=c(seq(1e-10,1e-2,length.out=nGenes-100),seq(1e-2,.2,length.out=50),seq(50)) names(pScreen)=names(table(genes)) #discards genes that are not simulated pConfirmation=matrix(runif(1000),nrow=1000,ncol=1) rownames(pConfirmation)=transcripts stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation ,pScreenAdjusted=TRUE, tx2gene=tx2gene) stageRObj <- stageWiseAdjustment(stageRObj, method="dte", alpha=0.05) head(getSignificantGenes(stageRObj))