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YuLab-SMU / clusterProfiler

:bar_chart: A universal enrichment tool for interpreting omics data
https://yulab-smu.top/biomedical-knowledge-mining-book/
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gsePathway not found #736

Open NicoHadas opened 2 days ago

NicoHadas commented 2 days ago

Thank you for the great package!

Sorry if I missed an update, but it seems like gsePathway() function no longer works.

Upregulated.R <- gsePathway(Upregulated.GeneList) Error in gsePathway(Upregulated.GeneList) : could not find function "gsePathway"

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[1] /home/nico/R/x86_64-pc-linux-gnu-library/4.4 [2] /usr/local/lib/R/site-library [3] /usr/lib/R/site-library [4] /usr/lib/R/library

V ── Loaded and on-disk version mismatch.

─ Python configuration ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── python: /home/nico/.virtualenvs/r-reticulate/bin/python libpython: /usr/lib/python3.12/config-3.12-x86_64-linux-gnu/libpython3.12.so pythonhome: /home/nico/.virtualenvs/r-reticulate:/home/nico/.virtualenvs/r-reticulate version: 3.12.3 (main, Sep 11 2024, 14:17:37) [GCC 13.2.0] numpy: /home/nico/.virtualenvs/r-reticulate/lib/python3.12/site-packages/numpy numpy_version: 2.0.0 pandas: /home/nico/.virtualenvs/r-reticulate/lib/python3.12/site-packages/pandas

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Regards

guidohooiveld commented 1 day ago

What you missed is that the function gsePathway is part of the package ReactomePA , and not clusterProfiler. :-)

> library(clusterProfiler)
> 
> data(geneList, package = "DOSE")
> yy <-  gsePathway(geneList, organism = "human", eps=0)
Error in gsePathway(geneList, organism = "human", eps = 0) : 
  could not find function "gsePathway"
> 
> library(ReactomePA)
ReactomePA v1.48.0  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use ReactomePA in published research, please cite:
Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479
> yy <-  gsePathway(geneList, organism = "human", eps=0)
>
> <<snip>>
>
> yy
#
# Gene Set Enrichment Analysis
#
#...@organism    human 
#...@setType     Reactome 
#...@keytype     ENTREZID 
#...@geneList    Named num [1:12495] 4.57 4.51 4.42 4.14 3.88 ...
 - attr(*, "names")= chr [1:12495] "4312" "8318" "10874" "55143" ...
#...nPerm        
#...pvalues adjusted by 'BH' with cutoff <0.05 
#...316 enriched terms found
'data.frame':   316 obs. of  11 variables:
 $ ID             : chr  "R-HSA-69278" "R-HSA-69620" "R-HSA-68882" "R-HSA-2555396" ...
 $ Description    : chr  "Cell Cycle, Mitotic" "Cell Cycle Checkpoints" "Mitotic Anaphase" "Mitotic Metaphase and Anaphase" ...
 $ setSize        : int  458 237 199 200 325 142 136 124 134 110 ...
 $ enrichmentScore: num  0.607 0.668 0.648 0.65 0.548 ...
 $ NES            : num  2.91 3.04 2.92 2.92 2.58 ...
 $ pvalue         : num  3.45e-49 1.00e-35 1.14e-27 3.33e-27 1.09e-25 ...
 $ p.adjust       : num  5.28e-46 7.65e-33 5.80e-25 1.27e-24 3.33e-23 ...
 $ qvalue         : num  3.99e-46 5.79e-33 4.39e-25 9.61e-25 2.52e-23 ...
 $ rank           : num  1769 1905 1857 1857 1857 ...
 $ leading_edge   : chr  "tags=36%, list=14%, signal=32%" "tags=43%, list=15%, signal=37%" "tags=39%, list=15%, signal=34%" "tags=40%, list=15%, signal=34%" ...
 $ core_enrichment: chr  "8318/55143/55388/991/2305/9493/1062/4605/9133/10403/7153/23397/6241/11065/220134/22974/4751/79019/55839/27338/8"| __truncated__ "8318/55143/55388/991/1062/9133/10403/11065/220134/79019/55839/27338/890/983/54821/4085/81930/332/9212/1111/891/"| __truncated__ "55143/991/1062/9133/10403/11065/220134/79019/55839/27338/983/54821/4085/81930/332/9212/891/9232/4001/11004/5347"| __truncated__ "55143/991/1062/9133/10403/11065/220134/79019/55839/27338/983/54821/4085/81930/332/9212/891/9232/4001/11004/5347"| __truncated__ ...
#...Citation
Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. 2016, 12(2):477-479 

> 
> dotplot(yy)
>

image