isAdjusted {stageR} | R Documentation |
This functions returns a logical stating whether the p-values have already been adjusted according to the stage-wise method.
isAdjusted(object, ...) ## S4 method for signature 'stageR' isAdjusted(object, ...) ## S4 method for signature 'stageRTx' isAdjusted(object, ...)
object |
an object of the |
... |
Additional arguments |
A logical stating whether the p-values have already been adjusted according to the stage-wise method
stageRTx
: Has stage-wise adjustment already been performed on the object?
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
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) isAdjusted(stageRObj) stageRObj <- stageWiseAdjustment(stageRObj, method="holm", alpha=0.05) isAdjusted(stageRObj)