getResults: Get significance results according to a stage-wise analysis.

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

Description

This functions returns a matrix that indicates whether a specific feature is significant for a specific hypothesis of interest according to a stage-wise analysis. The function is not applicable to transcript-level analysis.

Usage

getResults(object, ...)

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

Arguments

object

an object of the stageRClass class.

Details

The FDR adjusted screening hypothesis p-values are compared to the alpha level specified. The FWER adjusted confirmation stage p-values are compared to the adjusted significance level from the screening stage.

Value

A logical matrix with rows corresponding to genes and columns corresponding to contrasts, where the first column represents the screening stage on the aggregated p-values. A 0 represents a non-significant test, a 1 represents a significant test according to the stage-wise analysis.

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)
head(getResults(stageRObj))

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