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

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/permutationPvalueCollectionGsea.R

Description

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

Usage

1
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

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##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 May 2, 2018, 4:30 a.m.