permutationPvalueCollectionGsea: Compute the GSEA p-values for a list of gene sets

Description

Compute the nominal p-value associated with a GSEA for a list of gene sets, from the outputs of the function collectionGsea.

Usage

permutationPvalueCollectionGsea(permScores, dataScores)

Arguments

permScores

a numeric matrix of permutation-based scores, of which each row is named and corresponds to a gene set, output from the function collectionGsea

dataScores

a named numeric vector of observed scores output from the function collectionGsea

Value

a named numeric vector of p-values, each of which corresponds to a gene set

References

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.

Examples

Run this code

##example 1
gl <- runif(100, min=0, max=5)
gl <- gl[order(gl, decreasing=TRUE)]
names(gl) <- as.character(sample(x=seq(from=1, to=100, by=1), size=100,
replace=FALSE))
gs1 <- sample(names(gl), size=20, replace=FALSE)
gs2 <- sample(names(gl), size=20, replace=FALSE)
gsc <- list(subset1=gs1, subset2=gs2)
GSCscores <- collectionGsea(collectionOfGeneSets=gsc, geneList=gl,
exponent=1, nPermutations=1000, minGeneSetSize=5)
GSCpvals <- permutationPvalueCollectionGsea(permScores=
GSCscores$Permutation.scores, dataScores=GSCscores$Observed.scores)
##example 2
## Not run: 
# library(KEGG.db)
# library(org.Dm.eg.db)
# ##load phenotype vector (see the vignette for details about the
# ##preprocessing of this data set)
# data("KcViab_Data4Enrich")
# DM_KEGG <- KeggGeneSets(species="Dm")
# GSCscores <- collectionGsea(collectionOfGeneSets=DM_KEGG, geneList=
# KcViab_Data4Enrich, exponent=1, nPermutations=1000, minGeneSetSize=100)
# GSCpvals <- permutationPvalueCollectionGsea(permScores=
# GSCscores$Permutation.scores, dataScores=GSCscores$Observed.scores)
# ## End(Not run)