stageRTx {stageR} | R Documentation |
Constructor function for stageRTxClass
. A stageR class is a class used for stage-wise analysis in high throughput settings.
In its most basic form, it consists of a vector of p-values for the screening hypothesis, a matrix of p-values for the confirmation hypotheses and a tx2gene object for linking genes to transcripts.
stageRTx(pScreen, pConfirmation, pScreenAdjusted = FALSE, tx2gene)
pScreen |
A vector of screening hypothesis p-values. |
pConfirmation |
A matrix of confirmation hypothesis p-values. The number of rows should be equal to the length of |
pScreenAdjusted |
logical, indicating whether the supplied p-values for the screening hypothesis have already been adjusted for multiplicity according to the FDR. |
tx2gene |
Only applicable for transcript-level analysis. A |
... |
Additional arguments. |
An instance of an object of the stageRTxClass
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
# create a \code{\link{stageRClass}} object pScreen <- runif(10) names(pScreen) <- paste0("gene",1:10) pConfirmation <- matrix(runif(30),nrow=10,ncol=3) rownames(pConfirmation) <- paste0("gene",1:10) stageRObj <- stageR(pScreen=pScreen, pConfirmation=pConfirmation) pConfirmationTx <- matrix(runif(10),ncol=1) names(pScreen) <- paste0("gene",rep(1:2,each=5)) stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmationTx, tx2gene=data.frame(transcripts=paste0("transcript",1:10),genes=paste0("gene",rep(1:2,each=5))))