permutationPvalueCollectionGsea {HTSanalyzeR} | R Documentation

## 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

### 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)

[Package HTSanalyzeR version 2.38.0 Index]