getAlpha: Retrieve the significance level for the stage-wise...

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

Description

This functions returns the significance level on which the stage-wise adjustment is based.

Usage

getAlpha(object, ...)

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

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

Arguments

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

Value

Returns a calar vector with the OFDR alpha level that was specified by the user.

Methods (by class)

• stageRTx: Retrieve the significance level for the stage-wise adjustment.

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)
stageRObj <- stageWiseAdjustment(stageRObj, method="holm", alpha=0.05)
getAlpha(stageRObj)

stageR documentation built on Nov. 8, 2020, 4:56 p.m.