stageWiseAdjustment: adjust p-values in a two-stage analysis

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

Description

This function will adjust p-values according to a hierarchical two-stage testing paradigm.

Usage

stageWiseAdjustment(object, method, alpha, ...)

## S4 method for signature 'stageR,character,numeric'
stageWiseAdjustment(object, method, alpha,
  adjustment = NULL, ...)

## S4 method for signature 'stageRTx,character,numeric'
stageWiseAdjustment(object, method,
  alpha, tx2gene, ...)

Arguments

object	an object of the stageRClass class.
method	Character string indicating the method used for FWER correction in the confirmation stage of the stage-wise analysis. Can be any of "none", "holm", "dte", "dtu", "user". "none" will not adjust the p-values in the confirmation stage. "holm" is an adapted Holm procedure for a stage-wise analysis, where the method takes into account the fact that genes in the confirmation stage have already passed the screening stage, hence the procedure will be more powerful for the most significant p-value as compared to the standard Holm procedure. "dte" is the adjusted Holm-Shaffer procedure for differential transcript expression analysis. "dtu" is the adjusted Holm-Shaffer procedure for differential transcript usage. "user" indicates a user-defined adjustment that should be specified with the adjustment argument.
alpha	the OFDR on which to control the two-stage analysis.
...	Additional arguments passed to .stageWiseTest
adjustment	a user-defined adjustment of the confirmation stage p-values. Only applicable when method is "user" and ignored otherwise.
tx2gene	Only applicable when method is "dte" or "dtu". A data.frame with transcript IDs in the first columns and gene IDs in the second column. The rownames from pConfirmation must be contained in the transcript IDs from tx2gene, and the names from pScreen must be contained in the gene IDs.

Value

A stageR/stageRTx object with stage-wise adjusted p-values.

Methods (by class)

• object = stageRTx,method = character,alpha = numeric: Adjust p-values in a two-stage 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 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.

S. Holm, "A Simple Sequentially Rejective Multiple Test Procedure," Scandinavian Journal of Statistics, vol. 6, no. 2, pp. 65-70, 1979. J. P. Shaffer, "Modified Sequentially Rejective Multiple Test Procedures," Journal of the American Statistical Association, vol. 81, p. 826, 1986.

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

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