adjustedAlphaLevel: Get adjusted significance level from the screening stage.
In stageR: stageR: stage-wise analysis of high throughput gene expression data in R

Description Usage Arguments Details Value Methods (by class) References See Also Examples

This functions returns the adjusted significance level from the screening stage that should be used to compare confirmation stage FWER adjusted p-values against.

adjustedAlphaLevel(object, ...)

## S4 method for signature 'stageR'
adjustedAlphaLevel(object)

## S4 method for signature 'stageRTx'
adjustedAlphaLevel(object)

object

an object of the stageRClass class.

The adjusted significance level is calculated as the fraction of significant features in the screening stage multiplied the alpha level.

Scalar, the adjusted significance level from the screening stage.

stageRTx: Get adjusted significance level from the screening stage.

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

R. Heller, E. Manduchi, G. R. Grant, and W. J. Ewens, "A flexible two-stage procedure for identifying gene sets that are differentially expressed." Bioinformatics (Oxford, England), vol. 25, pp. 1019-25, 2009.

stageR, stageRClass

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, pScreenAdjusted=FALSE)
stageRObj <- stageWiseAdjustment(stageRObj, method="holm", alpha=0.05)
adjustedAlphaLevel(stageRObj)
# @method stageR-method