getMethod {stageR} | R Documentation |
This functions retrieves the method used for FWER multiple testing correction in the confirmation stage of a stage-wise analysis.
getMethod(object, ...) ## S4 method for signature 'stageR' getMethod(object, ...) ## S4 method for signature 'stageRTx' getMethod(object, ...)
object |
an object of the |
... |
Additional arguments |
Returns a character vector of length 1 specifying the FWER correction method that is used in the confirmation stage of the stage-wise analysis.
stageRTx
: Retrieve FWER correction method.
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) stageRObj <- stageWiseAdjustment(stageRObj, method="holm", alpha=0.05) getMethod(stageRObj)