This functions returns a matrix that indicates whether a specific feature is significant for a specific hypothesis of interest according to a stage-wise analysis. The function is not applicable to transcript-level analysis.
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an object of the
The FDR adjusted screening hypothesis p-values are compared to the alpha level specified. The FWER adjusted confirmation stage p-values are compared to the adjusted significance level from the screening stage.
A logical matrix with rows corresponding to genes and columns corresponding to contrasts, where the first column represents the screening stage on the aggregated p-values. A 0 represents a non-significant test, a 1 represents a significant test according to the stage-wise analysis.
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
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pScreen=c(seq(1e-10,1e-2,length.out=100),seq(1e-2,.2,length.out=100),seq(.2,1,length.out=100)) names(pScreen)=paste0("gene",1:300) pConfirmation=matrix(runif(900),nrow=300,ncol=3) dimnames(pConfirmation)=list(paste0("gene",1:300),c("H1","H2","H3")) stageRObj <- stageR(pScreen=pScreen, pConfirmation=pConfirmation) stageRObj <- stageWiseAdjustment(stageRObj, method="holm", alpha=0.05) head(getResults(stageRObj))
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