stageR: Create stageR object

In statOmics/stageR: stageR: stage-wise analysis of high throughput gene expression data in R

Description

Constructor function for stageRClass. 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 and a matrix of p-values for the confirmation hypotheses.

Usage

stageR(pScreen, pConfirmation, pScreenAdjusted = FALSE)

Arguments

pScreen	A vector of screening hypothesis p-values.
pConfirmation	A matrix of confirmation hypothesis p-values. When constructing a stageRClass object, the number of rows should be equal to the length of pScreen. For a stageRTxClass object, the dimensions can be different.
pScreenAdjusted	logical, indicating whether the supplied p-values for the screening hypothesis have already been adjusted for multiplicity according to the FDR.
...	Additional arguments.

Value

An instance of an object of the stageRClass

References

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

Examples

# 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))))

statOmics/stageR documentation built on Dec. 15, 2021, 2:58 a.m.