getAdjustedPValues {stageR} | R Documentation |
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.
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, ...)
object |
an object of the |
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 |
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.
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.
object = stageRTx,onlySignificantGenes = logical,order = logical
: Retrieve the stage-wise adjusted p-values.
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
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))