getAdjustedPValues: Retrieve the stage-wise adjusted p-values.

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

Description

This functions returns the stage-wise adjusted p-values for an object from the stageRClass class. Note, that the p-values should have been adjusted with the stageWiseAdjustment,stageR,character,numeric-method function prior to calling this function.

Usage

getAdjustedPValues(object, onlySignificantGenes, order, ...)

## S4 method for signature 'stageR,logical,logical'
getAdjustedPValues(object,
  onlySignificantGenes, order, ...)

## S4 method for signature 'stageRTx,logical,logical'
getAdjustedPValues(object,
  onlySignificantGenes, order, ...)

Arguments

object	an object of the stageRClass class.
onlySignificantGenes	logical. If FALSE (default), all genes are returned. If TRUE, only the genes significant for the screening hypothesis are returned.
order	logical. If TRUE (default), the returned matrix of adjusted p-values are ordered based on the screening hypothesis adjusted p-value.
...	Other arguments passed to .getAdjustedP or .getAdjustedPTx

Details

The function returns FDR adjusted p-values for the screening hypothesis and stage-wise adjusted p-values for the confirmation hypothesis p-values. For features that were not significant in the screening hypothesis, the confirmation stage adjusted p-values are set to NA. The adjusted p-values in the output of getAdjustedPValues can directly be compared to alpha, the OFDR level specified in stageWiseAdjustment, to flag significant features.

Value

For complex DGE experiments (stageR object), a matrix of adjusted p-values where every row corresponds to a gene, and every column corresponds to a contrast. The first column will be the BH FDR adjusted p-value from the screening step. For transcript-level experiments (stageRTx object), a matrix of adjusted p-values where every row corresponds to a transcript.

Methods (by class)

• object = stageRTx,onlySignificantGenes = logical,order = logical: Retrieve the stage-wise adjusted p-values.

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(getAdjustedPValues(stageRObj, onlySignificantGenes=TRUE, order=TRUE))

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