stageRTx: Create stageRTx object.

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

Description

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.

Usage

stageRTx(pScreen, pConfirmation, pScreenAdjusted = FALSE, tx2gene)

Arguments

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 pScreen.
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 data.frame with transcript IDs in the first columns and gene IDs in the second column. The rownames from pConfirmation must be contained in the transcript IDs from tx2gene, and the names from pScreen must be contained in the gene IDs.
...	Additional arguments.

Value

An instance of an object of the stageRTxClass

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.