isAdjusted: Has stage-wise adjustment already been performed on the...

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

Description

This functions returns a logical stating whether the p-values have already been adjusted according to the stage-wise method.

Usage

isAdjusted(object, ...)

## S4 method for signature 'stageR'
isAdjusted(object, ...)

## S4 method for signature 'stageRTx'
isAdjusted(object, ...)

Arguments

object	an object of the stageRClass or stageRTxClass class.
...	Additional arguments

Value

A logical stating whether the p-values have already been adjusted according to the stage-wise method

Methods (by class)

• stageRTx: Has stage-wise adjustment already been performed on the object?

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

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)

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