adjustedAlphaLevel: Get adjusted significance level from the screening stage.

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

Description

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

Usage

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adjustedAlphaLevel(object, ...)

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

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

Arguments

object

an object of the stageRClass class.

Details

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

Value

Scalar, the adjusted significance level from the screening stage.

Methods (by class)

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

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.

See Also

stageR, stageRClass

Examples

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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

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