FDRcollectionGsea {HTSanalyzeR} | R Documentation |
This function computes the GSEA fdr over a list of gene sets
FDRcollectionGsea(permScores, dataScores)
permScores |
a numeric matrix of permutation-based scores resulting from the output of collectionGsea |
dataScores |
a named numeric vector of observed scores resulting from the output of collectionGsea |
a named numeric vector of FDR, one for each gene set
Camille Terfve, Xin Wang
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.
collectionGsea
, permutationPvalueCollectionGsea
##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) gscs <- list(gs1=gs1, gs2=gs2) GSCscores <- collectionGsea(collectionOfGeneSets=gscs, geneList=gl, exponent=1, nPermutation=1000, minGeneSetSize=5) GSCfdrs <- FDRcollectionGsea(permScores=GSCscores$Permutation.scores, dataScores=GSCscores$Observed.scores) ##example 2 (see the vignette for details about the preprocessing of this ##data set) ## Not run: library(org.Dm.eg.db) library(KEGG.db) data("KcViab_Data4Enrich") DM_KEGG <- KeggGeneSets(species="Dm") GSCscores <- collectionGsea(collectionOfGeneSets=DM_KEGG, geneList= KcViab_Data4Enrich, exponent=1, nPermutations=1000, minGeneSetSize=100) GSCfdrs <- FDRcollectionGsea(permScores=GSCscores$Permutation.scores, dataScores=GSCscores$Observed.scores) ## End(Not run)