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

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

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

Author(s)

Camille Terfve, Xin Wang

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.

See Also

collectionGsea

Examples

##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)

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.