adjustedAlphaLevel {stageR} | R Documentation |
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 |
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.
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