Comments (4)
guidohooiveld
commented on August 16, 2024
Does it work with the example code (since your code as such is not reproducible)? What is your sessionInfo()?
> library(clusterProfiler)
> data(gcSample)
> xx <- compareCluster(gcSample, fun=enrichKEGG,
+ organism="hsa", pvalueCutoff=0.05)
> xx
#
# Result of Comparing 8 gene clusters
#
#.. @fun enrichKEGG
#.. @geneClusters List of 8
$ X1: chr [1:216] "4597" "7111" "5266" "2175" ...
$ X2: chr [1:805] "23450" "5160" "7126" "26118" ...
$ X3: chr [1:392] "894" "7057" "22906" "3339" ...
$ X4: chr [1:838] "5573" "7453" "5245" "23450" ...
$ X5: chr [1:929] "5982" "7318" "6352" "2101" ...
$ X6: chr [1:585] "5337" "9295" "4035" "811" ...
$ X7: chr [1:582] "2621" "2665" "5690" "3608" ...
$ X8: chr [1:237] "2665" "4735" "1327" "3192" ...
#...Result 'data.frame': 76 obs. of 12 variables:
$ Cluster : Factor w/ 8 levels "X1","X2","X3",..: 2 2 2 3 3 3 4 4 4 4 ...
$ category : chr "Human Diseases" "Human Diseases" "Cellular Processes" "Environmental Information Processing" ...
$ subcategory: chr "Infectious disease: viral" "Immune disease" "Cell growth and death" "Signaling molecules and interaction" ...
$ ID : chr "hsa05169" "hsa05340" "hsa04110" "hsa04512" ...
$ Description: chr "Epstein-Barr virus infection" "Primary immunodeficiency" "Cell cycle" "ECM-receptor interaction" ...
$ GeneRatio : chr "23/406" "8/406" "18/406" "9/193" ...
$ BgRatio : chr "202/8662" "38/8662" "157/8662" "89/8662" ...
$ pvalue : num 6.83e-05 3.07e-04 3.83e-04 1.53e-04 3.29e-04 ...
$ p.adjust : num 0.0214 0.0399 0.0399 0.0362 0.0362 ...
$ qvalue : num 0.0199 0.0372 0.0372 0.0335 0.0335 ...
$ geneID : chr "4067/3383/7128/1869/890/1871/578/864/637/9641/6891/355/9134/5971/916/956/6850/7187/3551/919/4734/958/6772" "100/6891/3932/973/916/925/958/64421" "991/1869/890/1871/701/990/10926/9088/8317/9700/9134/1029/2810/699/11200/23594/8555/4173" "7057/3339/1299/3695/1101/3679/3910/3696/3693" ...
$ Count : int 23 8 18 9 17 19 17 10 22 19 ...
#.. number of enriched terms found for each gene cluster:
#.. X1: 0
#.. X2: 3
#.. X3: 3
#.. X4: 22
#.. X5: 10
#.. X6: 1
#.. X7: 17
#.. X8: 20
#
#...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
>
from clusterprofiler.
gongxin8888
commented on August 16, 2024
Hi Guido,
It does work with the following example but not with fun = enricher. I found alternative where I created a customized function with enricher. With that function, it works for me.
Thanks and have a great day!
GongXin
From: Guido Hooiveld ***@***.***>
Date: Thursday, February 22, 2024 at 2:05 AM
To: YuLab-SMU/clusterProfiler ***@***.***>
Cc: Yu, Gongxin ***@***.***>, Author ***@***.***>
Subject: [EXTERNAL] [MARKETING] Re: [YuLab-SMU/clusterProfiler] problem in run compareCluster (Issue #669)
Does it work with the example code (since your code as such is not reproducible)? What is your sessionInfo()?
library(clusterProfiler)
data(gcSample)
xx <- compareCluster(gcSample, fun=enrichKEGG,
+ organism="hsa", pvalueCutoff=0.05)
xx
#
# Result of Comparing 8 gene clusters
#
#.. @fun enrichKEGG
#.. @geneClusters List of 8
$ X1: chr [1:216] "4597" "7111" "5266" "2175" ...
$ X2: chr [1:805] "23450" "5160" "7126" "26118" ...
$ X3: chr [1:392] "894" "7057" "22906" "3339" ...
$ X4: chr [1:838] "5573" "7453" "5245" "23450" ...
$ X5: chr [1:929] "5982" "7318" "6352" "2101" ...
$ X6: chr [1:585] "5337" "9295" "4035" "811" ...
$ X7: chr [1:582] "2621" "2665" "5690" "3608" ...
$ X8: chr [1:237] "2665" "4735" "1327" "3192" ...
#...Result 'data.frame': 76 obs. of 12 variables:
$ Cluster : Factor w/ 8 levels "X1","X2","X3",..: 2 2 2 3 3 3 4 4 4 4 ...
$ category : chr "Human Diseases" "Human Diseases" "Cellular Processes" "Environmental Information Processing" ...
$ subcategory: chr "Infectious disease: viral" "Immune disease" "Cell growth and death" "Signaling molecules and interaction" ...
$ ID : chr "hsa05169" "hsa05340" "hsa04110" "hsa04512" ...
$ Description: chr "Epstein-Barr virus infection" "Primary immunodeficiency" "Cell cycle" "ECM-receptor interaction" ...
$ GeneRatio : chr "23/406" "8/406" "18/406" "9/193" ...
$ BgRatio : chr "202/8662" "38/8662" "157/8662" "89/8662" ...
$ pvalue : num 6.83e-05 3.07e-04 3.83e-04 1.53e-04 3.29e-04 ...
$ p.adjust : num 0.0214 0.0399 0.0399 0.0362 0.0362 ...
$ qvalue : num 0.0199 0.0372 0.0372 0.0335 0.0335 ...
$ geneID : chr "4067/3383/7128/1869/890/1871/578/864/637/9641/6891/355/9134/5971/916/956/6850/7187/3551/919/4734/958/6772" "100/6891/3932/973/916/925/958/64421" "991/1869/890/1871/701/990/10926/9088/8317/9700/9134/1029/2810/699/11200/23594/8555/4173" "7057/3339/1299/3695/1101/3679/3910/3696/3693" ...
$ Count : int 23 8 18 9 17 19 17 10 22 19 ...
#.. number of enriched terms found for each gene cluster:
#.. X1: 0
#.. X2: 3
#.. X3: 3
#.. X4: 22
#.. X5: 10
#.. X6: 1
#.. X7: 17
#.. X8: 20
#
#...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
—
Reply to this email directly, view it on GitHub<https://clicktime.symantec.com/15uBY59P1XknJ2h1XxDBg?h=3NwhEW4cTh29LHWJy6FoU6bSGd6OaiJo5FGJpbfodJA=&u=https://github.com/YuLab-SMU/clusterProfiler/issues/669%23issuecomment-1958828750>, or unsubscribe<https://clicktime.symantec.com/15uBcuLfU9SNhyWw5WcLJ?h=ZtNZrpbmKFShDmL967bWnQic1Bek6T43y6v8u65cLeM=&u=https://github.com/notifications/unsubscribe-auth/BGJSULBROUYKEEI2KRHCLP3YU3U4BAVCNFSM6AAAAABDRPQ3X6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJYHAZDQNZVGA>.
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guidohooiveld
commented on August 16, 2024
Happy to hear you got it somehow working, but to show for the record/archive that compareCluster also works with the generic function enricher:
> library(clusterProfiler)
>
> ## load some example data
> data(gcSample)
>
> ## manually download KEGG data; to be used as input for TERM2GENE and TERM2NAME
> kegg.data <- download_KEGG(species="hsa", keggType = "KEGG", keyType = "kegg")
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
> gene.sets <- kegg.data$KEGGPATHID2EXTID; colnames(gene.sets) <- c("PathwayID","GeneID")
> set.names <- kegg.data$KEGGPATHID2NAME; colnames(set.names) <- c("PathwayID","Description")
>
> ## run compareCluster with generic function enricher
> yy <- compareCluster(geneClusters = gcSample,
+ fun = "enricher",
+ minGSSize = 10,
+ maxGSSize = 500,
+ pvalueCutoff = 1,
+ pAdjustMethod = "BH",
+ TERM2GENE = gene.sets[, c("PathwayID","GeneID") ], #proper order columns
+ TERM2NAME = set.names[, c("PathwayID","Description") ]
+ )
>
> ## check
> yy
#
# Result of Comparing 8 gene clusters
#
#.. @fun enricher
#.. @geneClusters List of 8
$ X1: chr [1:216] "4597" "7111" "5266" "2175" ...
$ X2: chr [1:805] "23450" "5160" "7126" "26118" ...
$ X3: chr [1:392] "894" "7057" "22906" "3339" ...
$ X4: chr [1:838] "5573" "7453" "5245" "23450" ...
$ X5: chr [1:929] "5982" "7318" "6352" "2101" ...
$ X6: chr [1:585] "5337" "9295" "4035" "811" ...
$ X7: chr [1:582] "2621" "2665" "5690" "3608" ...
$ X8: chr [1:237] "2665" "4735" "1327" "3192" ...
#...Result 'data.frame': 226 obs. of 10 variables:
$ Cluster : Factor w/ 8 levels "X1","X2","X3",..: 1 1 1 2 2 2 2 2 2 2 ...
$ ID : chr "hsa04061" "hsa05146" "hsa04060" "hsa05169" ...
$ Description: chr "Viral protein interaction with cytokine and cytokine receptor" "Amoebiasis" "Cytokine-cytokine receptor interaction" "Epstein-Barr virus infection" ...
$ GeneRatio : chr "6/103" "6/103" "10/103" "23/406" ...
$ BgRatio : chr "100/8661" "102/8661" "297/8661" "202/8661" ...
$ pvalue : num 1.18e-03 1.31e-03 2.72e-03 6.84e-05 3.08e-04 ...
$ p.adjust : num 0.1283 0.1283 0.1778 0.0214 0.04 ...
$ qvalue : num 0.1206 0.1206 0.1671 0.0199 0.0373 ...
$ geneID : chr "6364/3559/2921/8793/3576/6374" "7850/2921/6317/3576/1281/22798" "7850/653/6364/3559/3595/2921/8793/10663/3576/6374" "4067/3383/7128/1869/890/1871/578/864/637/9641/6891/355/9134/5971/916/956/6850/7187/3551/919/4734/958/6772" ...
$ Count : int 6 6 10 23 8 18 22 13 12 14 ...
#.. number of enriched terms found for each gene cluster:
#.. X1: 3
#.. X2: 20
#.. X3: 5
#.. X4: 76
#.. X5: 48
#.. X6: 4
#.. X7: 36
#.. X8: 34
#
#...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
>
from clusterprofiler.
gongxin8888
commented on August 16, 2024
Thanks very much, Guido.
From: Guido Hooiveld ***@***.***>
Date: Friday, February 23, 2024 at 3:27 AM
To: YuLab-SMU/clusterProfiler ***@***.***>
Cc: Yu, Gongxin ***@***.***>, Author ***@***.***>
Subject: [EXTERNAL] [MARKETING] Re: [YuLab-SMU/clusterProfiler] problem in run compareCluster (Issue #669)
Happy to hear you got it somehow working, but to show for the record/archive that compareCluster also works with the generic function enricher:
library(clusterProfiler)
## load some example data
data(gcSample)
## manually download KEGG data; to be used as input for TERM2GENE and TERM2NAME
kegg.data <- download_KEGG(species="hsa", keggType = "KEGG", keyType = "kegg")
Reading KEGG annotation online: "https://clicktime.symantec.com/15tpP1jeVTHfBythNbPJs?h=BvATC_yQZMgUbXgJSVTTYf9I6zuqB-DfSvLHI1bdQ9Q=&u=https://rest.kegg.jp/link/hsa/pathway"...
Reading KEGG annotation online: "https://clicktime.symantec.com/15tpTqvvx4yFbvicv9nTV?h=gyLsJHDvW1i_tvMDv-e_jIqbdEUXLf48ayKIJRXZzyA=&u=https://rest.kegg.jp/list/pathway/hsa"...
gene.sets <- kegg.data$KEGGPATHID2EXTID; colnames(gene.sets) <- c("PathwayID","GeneID")
set.names <- kegg.data$KEGGPATHID2NAME; colnames(set.names) <- c("PathwayID","Description")
## run compareCluster with generic function enricher
yy <- compareCluster(geneClusters = gcSample,
+ fun = "enricher",
+ minGSSize = 10,
+ maxGSSize = 500,
+ pvalueCutoff = 1,
+ pAdjustMethod = "BH",
+ TERM2GENE = gene.sets[, c("PathwayID","GeneID") ], #proper order columns
+ TERM2NAME = set.names[, c("PathwayID","Description") ]
+ )
## check
yy
#
# Result of Comparing 8 gene clusters
#
#.. @fun enricher
#.. @geneClusters List of 8
$ X1: chr [1:216] "4597" "7111" "5266" "2175" ...
$ X2: chr [1:805] "23450" "5160" "7126" "26118" ...
$ X3: chr [1:392] "894" "7057" "22906" "3339" ...
$ X4: chr [1:838] "5573" "7453" "5245" "23450" ...
$ X5: chr [1:929] "5982" "7318" "6352" "2101" ...
$ X6: chr [1:585] "5337" "9295" "4035" "811" ...
$ X7: chr [1:582] "2621" "2665" "5690" "3608" ...
$ X8: chr [1:237] "2665" "4735" "1327" "3192" ...
#...Result 'data.frame': 226 obs. of 10 variables:
$ Cluster : Factor w/ 8 levels "X1","X2","X3",..: 1 1 1 2 2 2 2 2 2 2 ...
$ ID : chr "hsa04061" "hsa05146" "hsa04060" "hsa05169" ...
$ Description: chr "Viral protein interaction with cytokine and cytokine receptor" "Amoebiasis" "Cytokine-cytokine receptor interaction" "Epstein-Barr virus infection" ...
$ GeneRatio : chr "6/103" "6/103" "10/103" "23/406" ...
$ BgRatio : chr "100/8661" "102/8661" "297/8661" "202/8661" ...
$ pvalue : num 1.18e-03 1.31e-03 2.72e-03 6.84e-05 3.08e-04 ...
$ p.adjust : num 0.1283 0.1283 0.1778 0.0214 0.04 ...
$ qvalue : num 0.1206 0.1206 0.1671 0.0199 0.0373 ...
$ geneID : chr "6364/3559/2921/8793/3576/6374" "7850/2921/6317/3576/1281/22798" "7850/653/6364/3559/3595/2921/8793/10663/3576/6374" "4067/3383/7128/1869/890/1871/578/864/637/9641/6891/355/9134/5971/916/956/6850/7187/3551/919/4734/958/6772" ...
$ Count : int 6 6 10 23 8 18 22 13 12 14 ...
#.. number of enriched terms found for each gene cluster:
#.. X1: 3
#.. X2: 20
#.. X3: 5
#.. X4: 76
#.. X5: 48
#.. X6: 4
#.. X7: 36
#.. X8: 34
#
#...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
—
Reply to this email directly, view it on GitHub<https://clicktime.symantec.com/15tpDMM5aDvUN6ErHUb1d?h=lXlIhAVFsDV9FcWoTSrRgv9GXCqfgeMLPu4llmIqe2U=&u=https://github.com/YuLab-SMU/clusterProfiler/issues/669%23issuecomment-1960910360>, or unsubscribe<https://clicktime.symantec.com/15tpJBYN2qc4n34mq2zAF?h=m9VBvawBx_BfclpIE-sJEcGQvxo8jaF4n0SsOZ4ACNw=&u=https://github.com/notifications/unsubscribe-auth/BGJSULCOOYZBQGSAYTQCOJ3YVBHG3AVCNFSM6AAAAABDRPQ3X6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRQHEYTAMZWGA>.
You are receiving this because you authored the thread.Message ID: ***@***.***>
This message (including any attachments) is intended only for the use of the individual or entity to which it is addressed and may contain information that is non-public, proprietary, privileged, confidential, and exempt from disclosure under applicable law or may constitute as attorney work product. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this communication is strictly prohibited. If you have received this communication in error, notify us immediately by telephone and (i) destroy this message if a facsimile or (ii) delete this message immediately if this is an electronic communication. Thank you.
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Related Issues (20)
- How to combine different compareCluster results? HOT 1
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- gson 格式在最新版 enrichKEGG中出错 HOT 4
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- All p-values are equal to 1 HOT 1
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