stageWiseAdjustment {stageR} | R Documentation |
This function will adjust p-values according to a hierarchical two-stage testing paradigm.
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, ...)
object |
an object of the |
method |
Character string indicating the method used for FWER correction in the confirmation stage of the stage-wise analysis. Can be any of |
alpha |
the OFDR on which to control the two-stage analysis. |
... |
Additional arguments passed to |
adjustment |
a user-defined adjustment of the confirmation stage p-values. Only applicable when |
tx2gene |
Only applicable when |
A stageR/stageRTx object with stage-wise adjusted p-values.
object = stageRTx,method = character,alpha = numeric
: Adjust p-values in a two-stage analysis
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.
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)