GSEA
gseaRes_all <- vector(mode = "list", length = length(validated_ind))
names(gseaRes_all) <- paste0("PCcluster_", validated_ind)
for (i in seq_along(validated_ind)) {
res <- msigdb_gsea(validated_ind[i], PCAmodel, category = "C2")
gseaRes_all[[i]] <- res
}
##
## Attaching package: 'BiocGenerics'
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## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
##
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##
## Encountered 1 from.IDs with >1 corresponding to.ID
## (the first to.ID was chosen for each of them)
## Excluded 2744 from.IDs without a corresponding to.ID
## Registered S3 methods overwritten by 'clusterProfiler.dplyr':
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## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize,
## gseaParam, : There are duplicate gene names, fgsea may produce unexpected
## results.
## no term enriched under specific pvalueCutoff...
## Warning: The `add` argument of `group_by()` is deprecated as of dplyr 1.0.0.
## Please use the `.add` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.
## Encountered 1 from.IDs with >1 corresponding to.ID
## (the first to.ID was chosen for each of them)
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## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize,
## gseaParam, : There are duplicate gene names, fgsea may produce unexpected
## results.
## Encountered 1 from.IDs with >1 corresponding to.ID
## (the first to.ID was chosen for each of them)
## Excluded 2744 from.IDs without a corresponding to.ID
## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize,
## gseaParam, : There are duplicate gene names, fgsea may produce unexpected
## results.
## Warning in fgseaMultilevel(...): For some of the pathways the P-values were
## likely overestimated. For such pathways log2err is set to NA.
## no term enriched under specific pvalueCutoff...
## Encountered 1 from.IDs with >1 corresponding to.ID
## (the first to.ID was chosen for each of them)
## Excluded 2744 from.IDs without a corresponding to.ID
## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize,
## gseaParam, : There are duplicate gene names, fgsea may produce unexpected
## results.
## Encountered 1 from.IDs with >1 corresponding to.ID
## (the first to.ID was chosen for each of them)
## Excluded 2744 from.IDs without a corresponding to.ID
## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize,
## gseaParam, : There are duplicate gene names, fgsea may produce unexpected
## results.
## no term enriched under specific pvalueCutoff...
sapply(gseaRes_all, dim)
## PCcluster_188 PCcluster_468 PCcluster_21 PCcluster_579 PCcluster_1166
## [1,] 0 65 0 616 0
## [2,] 10 13 10 13 10
sapply(gseaRes_all, pathwaySearch, "COLO")
## PCcluster_188 PCcluster_468 PCcluster_21 PCcluster_579 PCcluster_1166
## 0 1 0 2 0
sapply(gseaRes_all, pathwaySearch, "COLO", proportion = TRUE)
## PCcluster_188 PCcluster_468 PCcluster_21 PCcluster_579 PCcluster_1166
## NaN 0.015384615 NaN 0.003246753 NaN
for (i in seq_along(gseaRes_all)) {
res <- gseaRes_all[[i]]
gseaSub <- subsetGSEA(res, n = 20)
print(gseaBarplot(gseaRes = gseaSub))
print(gseaNetwork(gseaRes = gseaSub, similarity_metric = "overlap_similarity", similarity_cutoff = 0.3))
}
## [1] "No pathway is enriched"
## [1] "No pathway is enriched"
## [1] "No pathway is enriched"
## [1] "No pathway is enriched"
## [1] "No pathway is enriched"
## [1] "No pathway is enriched"
