guidohooiveld
commented
3 months ago FYI: when using the latest version of clusterProfiler, the function enrichWP works as expected....:
There has been an issue with WikiPathways few months ago, but that has been resolved.
> library(clusterProfiler)
> data(geneList, package='DOSE')
> de <- names(geneList)[1:100]
>
>
> yy <- enrichWP(de, organism= c("Homo sapiens"), pvalueCutoff=0.05, pAdjustMethod = "BH")
>
> yy
#
# over-representation test
#
#...@organism Homo sapiens
#...@ontology WikiPathways
#...@keytype ENTREZID
#...@gene chr [1:100] "4312" "8318" "10874" "55143" "55388" "991" "6280" "2305" ...
#...pvalues adjusted by 'BH' with cutoff <0.05
#...15 enriched terms found
'data.frame': 15 obs. of 9 variables:
$ ID : chr "WP2446" "WP2361" "WP179" "WP5039" ...
$ Description: chr "Retinoblastoma gene in cancer" "Gastric cancer network 1" "Cell cycle" "SARS CoV 2 innate immunity evasion and cell specific immune response" ...
$ GeneRatio : chr "9/60" "6/60" "7/60" "5/60" ...
$ BgRatio : chr "89/8421" "28/8421" "120/8421" "66/8421" ...
$ pvalue : num 1.04e-08 3.38e-08 2.07e-05 9.93e-05 1.18e-04 ...
$ p.adjust : num 1.78e-06 2.91e-06 1.19e-03 4.07e-03 4.07e-03 ...
$ qvalue : num 1.45e-06 2.37e-06 9.66e-04 3.31e-03 3.31e-03 ...
$ geneID : chr "8318/9133/7153/6241/890/983/81620/7272/1111" "4605/7153/11065/22974/6286/6790" "8318/991/9133/890/983/7272/1111" "3627/10563/6373/4283/3902" ...
$ Count : int 9 6 7 5 3 8 6 3 3 3 ...
#...Citation
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.
The Innovation. 2021, 2(3):100141
>
> as.data.frame(yy)[1:5,]
ID
WP2446 WP2446
WP2361 WP2361
WP179 WP179
WP5039 WP5039
WP4240 WP4240
Description
WP2446 Retinoblastoma gene in cancer
WP2361 Gastric cancer network 1
WP179 Cell cycle
WP5039 SARS CoV 2 innate immunity evasion and cell specific immune response
WP4240 Regulation of sister chromatid separation at the metaphase anaphase transition
GeneRatio BgRatio pvalue p.adjust qvalue
WP2446 9/60 89/8421 1.037133e-08 1.783869e-06 1.451987e-06
WP2361 6/60 28/8421 3.379083e-08 2.906011e-06 2.365358e-06
WP179 7/60 120/8421 2.069085e-05 1.186275e-03 9.655731e-04
WP5039 5/60 66/8421 9.930464e-05 4.072512e-03 3.314835e-03
WP4240 3/60 14/8421 1.183870e-04 4.072512e-03 3.314835e-03
geneID Count
WP2446 8318/9133/7153/6241/890/983/81620/7272/1111 9
WP2361 4605/7153/11065/22974/6286/6790 6
WP179 8318/991/9133/890/983/7272/1111 7
WP5039 3627/10563/6373/4283/3902 5
WP4240 991/1062/4085 3
>
> packageVersion("clusterProfiler")
[1] ‘4.10.1’
>
>
boutrys
Hello,
My code is not working anymore,
ego <- clusterProfiler::enrichWP(gene = base::unique(ids_geneList[,2]), organism = "Homo sapiens", universe = background_gene, pAdjustMethod = "BH", qvalueCutoff = cutoff)
and the error is as follow
Error in file(con, "r") : cannot open the connection to 'https://wikipathways-data.wmcloud.org/current/gmt/wikipathways-20240311-gmt-Homo_sapiens.gmt' In addition: Warning message: In file(con, "r") : cannot open URL 'https://data.wikipathways.org/current/gmt/wikipathways-20240311-gmt-Homo_sapiens.gmt': HTTP status was '404 Not Found'
Indeed I've checked
https://data.wikipathways.org/current/gmt/
and now I guess it should be wikipathways-20240310-gmt-Homo_sapiens.gmt (https://data.wikipathways.org/current/gmt/wikipathways-20240310-gmt-Homo_sapiens.gmt)
All files in wikipathways have been updated 3 das ago,
Can someone fix this please ?
Thanks in advance and wonderfull package by the way :)
Best,
Simon