Question

Issue of clusterprofiler package

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unique379 • 0

@unique379-10694

Last seen 8.0 years ago

its pity that your recent version does not work properly due to you have updated some functions and their arguments.

## changes in some functions that you made:

In bitr function:

previous it was "annoDb="org.Dr.eg.db"" and now it become "OrgDb".

In enrichGO function:

previous it was organism="zebrafish" " and now you changed into "OrgDb".

Note: Anyway i made changes into my script but i found its not working at all. PLEASE HELP AND FIX IT ASAP.

Even though, your example data seems does not executed:

For example.

data(gcSample)
yy <- enrichGO(gcSample[[1]], 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
head(summary(yy))
[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust    qvalue    
[8] geneID      Count     
<0 rows> (or 0-length row.names)

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
 [1] grid      parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] org.Dr.eg.db_3.3.0    gridExtra_2.2.1       plyr_1.8.4            pathview_1.12.0      
 [5] org.Hs.eg.db_3.3.0    KEGGprofile_1.14.0    stringi_1.1.2         magrittr_1.5         
 [9] igraph_1.0.1          networkD3_0.2.13      biomaRt_2.28.0        GO.db_3.3.0          
[13] AnnotationDbi_1.34.4  IRanges_2.6.1         Biobase_2.32.0        ReactomePA_1.16.2    
[17] clusterProfiler_3.0.5 DOSE_2.10.7           S4Vectors_0.10.3      BiocGenerics_0.18.0  
[21] BiocInstaller_1.22.3

loaded via a namespace (and not attached):
 [1] KEGGREST_1.12.3    qvalue_2.4.2       reshape2_1.4.2     splines_3.3.1     
 [5] lattice_0.20-34    colorspace_1.2-7   graphite_1.18.1    htmltools_0.3.5   
 [9] yaml_2.1.13        XML_3.98-1.4       DBI_0.5-1          Rgraphviz_2.16.0  
[13] rappdirs_0.3.1     topGO_2.24.0       matrixStats_0.51.0 KEGG.db_3.2.3     
[17] stringr_1.1.0      zlibbioc_1.18.0    Biostrings_2.40.2  munsell_0.4.3     
[21] GOSemSim_1.30.3    gtable_0.2.0       htmlwidgets_0.7    SparseM_1.74      
[25] curl_2.2           GSEABase_1.34.1    Rcpp_0.12.7        xtable_1.8-2      
[29] reactome.db_1.55.0 scales_0.4.0       DO.db_2.9          jsonlite_1.1      
[33] graph_1.50.0       annotate_1.50.1    XVector_0.12.1     TeachingDemos_2.10
[37] ggplot2_2.1.0      png_0.1-7          digest_0.6.10      tools_3.3.1       
[41] bitops_1.0-6       RCurl_1.95-4.8     tibble_1.2         RSQLite_1.0.0     
[45] tidyr_0.6.0        KEGGgraph_1.30.0   assertthat_0.1     httr_1.2.1        
[49] R6_2.2.0

clusterprofiler • 4.6k views

ADD COMMENT • link updated 8.1 years ago by Guangchuang Yu ★ 1.2k • written 8.1 years ago by unique379 • 0

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Entering edit mode

Hi,

Generally, the maintainer is reponsive on GitHub. He should also respond here.

You can create an issue at github.com/guangchuangyu/clusterprofiler/issues just to make sure he is aware.

Regards,

Marcel

ADD REPLY • link 8.1 years ago Marcel Ramos 700

score 1 · Answer 1 · 2016-11-18

From experience I also know clusterProfiler and related packages are indeed frequently updated to add new functionality, which IMHO is very nice. As a result the use of functions and their arguments are sometimes changed.

I agree with you that the example code on the help page of ?enrichGO doesn't work (anymore?). However, if you would have checked the online vignette here, you would have found the code below that indeed works.

Bottom line: you have to provide two arguments/character vectors that are the 'relevant' genes (gene) resp. the total set of genes you analyzed (names(geneList)).

> data(geneList, package="DOSE")
> gene <- names(geneList)[abs(geneList) > 2]
>
>
> yy <- enrichGO  (gene         = gene,
+                 universe      = names(geneList),
+                 OrgDb         = org.Hs.eg.db,
+                 ont           = "CC",
+                 pAdjustMethod = "BH",
+                 pvalueCutoff  = 0.01,
+                 qvalueCutoff  = 0.05,
+                 readable      = TRUE)
>
> head(summary(yy))
                   ID                              Description GeneRatio   BgRatio
GO:0005819 GO:0005819                                  spindle    24/199 231/11711
GO:0000793 GO:0000793                     condensed chromosome    17/199 156/11711
GO:0000779 GO:0000779 condensed chromosome, centromeric region    13/199  84/11711
GO:0005876 GO:0005876                      spindle microtubule    10/199  46/11711
GO:0005875 GO:0005875           microtubule associated complex    14/199 110/11711
GO:0000776 GO:0000776                              kinetochore    13/199 101/11711
                 pvalue     p.adjust       qvalue
GO:0005819 9.909518e-13 2.427832e-10 2.148801e-10
GO:0000793 1.141749e-09 1.180866e-07 1.045149e-07
GO:0000779 1.445959e-09 1.180866e-07 1.045149e-07
GO:0005876 3.833921e-09 2.279256e-07 2.017300e-07
GO:0005875 4.651542e-09 2.279256e-07 2.017300e-07
GO:0000776 1.464436e-08 5.979781e-07 5.292524e-07
                                                                                                                                                  geneID
GO:0005819 CDCA8/CDC20/KIF23/CENPE/ASPM/DLGAP5/SKA1/NUSAP1/TPX2/NEK2/CDK1/MAD2L1/KIF18A/BIRC5/KIF11/TTK/AURKB/PRC1/KIFC1/KIF18B/KIF20A/AURKA/CCNB1/KIF4A
GO:0000793                                         CENPE/NDC80/TOP2A/NCAPH/HJURP/SKA1/NEK2/CENPM/CENPN/ERCC6L/MAD2L1/BIRC5/NCAPG/AURKB/CHEK1/AURKA/CCNB1
GO:0000779                                                                 CENPE/NDC80/HJURP/SKA1/NEK2/CENPM/CENPN/ERCC6L/MAD2L1/BIRC5/AURKB/AURKA/CCNB1
GO:0005876                                                                                   SKA1/NUSAP1/CDK1/KIF18A/KIF11/AURKB/PRC1/KIF18B/AURKA/KIF4A
GO:0005875                                                        CDCA8/KIF23/CENPE/KIF18A/BIRC5/KIF11/AURKB/KIFC1/KIF18B/KIF20A/AURKA/KIF4A/MAPT/DNALI1
GO:0000776                                                                CENPE/NDC80/HJURP/SKA1/NEK2/CENPM/CENPN/ERCC6L/MAD2L1/KIF18A/BIRC5/AURKB/CCNB1
           Count
GO:0005819    24
GO:0000793    17
GO:0000779    13
GO:0005876    10
GO:0005875    14
GO:0000776    13
Warning message:
In summary(yy) :
  summary method to convert the object to data.frame is deprecated, please use as.data.frame instead.
>

> sessionInfo()
R version 3.3.1 Patched (2016-10-18 r71535)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1


other attached packages:
[1] org.Hs.eg.db_3.4.0    AnnotationDbi_1.36.0  IRanges_2.8.1        
[4] S4Vectors_0.12.0      Biobase_2.34.0        BiocGenerics_0.20.0  
[7] clusterProfiler_3.2.5 DOSE_3.0.6           

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7        plyr_1.8.4         tools_3.3.1        RSQLite_1.0.0     
 [5] tibble_1.2         gtable_0.2.0       fastmatch_1.0-4    igraph_1.0.1      
 [9] DBI_0.5-1          fgsea_1.1.0.9000   gridExtra_2.2.1    stringr_1.1.0     
[13] grid_3.3.1         qvalue_2.6.0       data.table_1.9.6   BiocParallel_1.8.1
[17] GOSemSim_2.0.1     GO.db_3.4.0        ggplot2_2.2.0      DO.db_2.9         
[21] reshape2_1.4.2     tidyr_0.6.0        magrittr_1.5       scales_0.4.1      
[25] splines_3.3.1      assertthat_0.1     colorspace_1.3-0   stringi_1.1.2     
[29] lazyeval_0.2.0     munsell_0.4.3      chron_2.3-47      
>

score 0 · Answer 2 · 2016-11-18

0

Entering edit mode

Marcel Ramos 700

@marcel-ramos-7325

Last seen 5 weeks ago

United States

Hi,

Generally, the maintainer is reponsive on GitHub. He should also respond here.

You can create an issue at github.com/guangchuangyu/clusterprofiler/issues just to make sure he is aware.

Regards,

Marcel

ADD COMMENT • link 8.1 years ago Marcel Ramos 700

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Entering edit mode

for question, support site is prefer.

ADD REPLY • link 8.1 years ago Guangchuang Yu ★ 1.2k

score 0 · Answer 3 · 2016-11-20

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Entering edit mode

Guangchuang Yu ★ 1.2k

@guangchuang-yu-5419

Last seen 8 weeks ago

China/Guangzhou/Southern Medical Univer…

> yy <- enrichGO(gcSample[[1]], 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.05)
> head(yy)
                   ID                         Description GeneRatio   BgRatio
GO:0021978 GO:0021978       telencephalon regionalization     4/192 13/16672
GO:0061351 GO:0061351 neural precursor cell proliferation     9/192 127/16672
                 pvalue   p.adjust     qvalue
GO:0021978 1.123776e-05 0.02121357 0.01949709
GO:0061351 1.626184e-05 0.02121357 0.01949709
                                                   geneID Count
GO:0021978                            5080/9355/2016/2018     4
GO:0061351 4771/2173/5080/8326/64211/2047/2016/51176/2018     9

Actually it *works* if you set pvalueCutoff=0.05.

will update corresponding man file.

ADD COMMENT • link 8.1 years ago Guangchuang Yu ★ 1.2k

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Dear Guangc huang,

if you are saying this is working with the changing of pvalues. then why it is not working for my dataset of zebrafish? eventhough i have tested with different-2 values of pvalueCutoff=0.05,qvalueCutoff=0.1 and results its the same (Zero enrichment). IS THIS ISSUE OF DIFFERENT SPECIES ??

> enrich_go_bp <- enrichGO(gene=as.vector(x),OrgDb="org.Dr.eg.db",ont="BP", pvalueCutoff=0.05,qvalueCutoff=0.1, readable=TRUE, minGSSize = 5)
> head(summary(enrich_go_bp))
[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust    qvalue     
[8] Count      
<0 rows> (or 0-length row.names)
> enrich_go_cc <- enrichGO(gene=as.vector(x),OrgDb="org.Dr.eg.db",ont="CC", pvalueCutoff=0.05,qvalueCutoff=0.1, readable=TRUE, minGSSize = 5)
> head(summary(enrich_go_cc))
[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust    qvalue     
[8] Count      
<0 rows> (or 0-length row.names)
> enrich_go_mf <- enrichGO(gene=as.vector(x),OrgDb="org.Dr.eg.db",ont="MF", pvalueCutoff=0.05,qvalueCutoff=0.1, readable=TRUE, minGSSize = 5)
> head(summary(enrich_go_mf))
[1] ID          Description GeneRatio   BgRatio     pvalue      p.adjust    qvalue     
[8] Count      
<0 rows> (or 0-length row.names)

> head(as.vector(x))
[1] "561503" "368404" "140818" "378838" "81885"  "170455"

however, its working pretty well with the package goProfile and also it was working before in your last version of package "clusterProfiler", i really dont under stand whats wrong with this.

library(goProfiles)
goANY <- basicProfile(genelist=as.vector(x), onto='ANY', level=2, orgPackage="org.Dr.eg.db")

> print(goANY)
$MF
                                          Description       GOID Frequency
12                               antioxidant activity GO:0016209         2
9                                             binding GO:0005488       570
4                                  catalytic activity GO:0003824       350
15                           chemoattractant activity GO:0042056         0
17                            chemorepellent activity GO:0045499         1
14                          D-alanyl carrier activity GO:0036370         0
1                           electron carrier activity GO:0009055         3
13                          metallochaperone activity GO:0016530         0
19                       molecular function regulator GO:0098772        34
18                      molecular transducer activity GO:0060089        40
11                                 morphogen activity GO:0016015         0

ADD REPLY • link 8.1 years ago unique379 • 0

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see https://github.com/GuangchuangYu/clusterProfiler/wiki/FAQ#no-term-enriched

ADD REPLY • link 8.1 years ago Guangchuang Yu ★ 1.2k

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Ok i can understand that this could be a problem but i really disappointed that you always change parameters within your function. Recently i found another error on your enrichResults function, you just completely removed the list object of "geneIncategory" in recent your release. I have two different system where two different release was installed ‘3.0.5’ and '3.2.2' and in newest version you just abolish the "geneIncategory" object?? Gods knowns what else you have made changes in your recent release or what you are going to change. My pieline script just STOPED WORKING becasue of your new changes. PLEASE STOP CHANGING NAME OF PARAMETERS OR REMOVING PARAMETERS IN YOUR FUNCTION.

ADD REPLY • link 8.1 years ago unique379 • 0

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The only parameter change is to use OrgDb, which is for extending enrichGO to analyze all species that have OrgDb object. Not only for those already have a package provided by Bioconductor, but also for those can be queried online or built from online data. THIS IS REALLY AWESOME. IF YOU DON'T LIKE IT, USE OTHER PACKAGE. I REALLY DON'T CARE.

The right way is to depend a package is to use open API. Those functions not exported or slots that don't provide access methods are (mostly) intended for reasons. If you really need something that is not exported, give me your reasons and ask me to export. DON'T JUST COMPLAIN.

The geneInCategory slot was remove to save object size, since I find a good solution to make it as a *computed slot*. Now you can access it via geneInCategory(x).

IF YOU HAVE NO IDEA WHY THE PACKAGE EVOLVE, READ THE DOCUMENT. IF YOU CAN'T FIGURE OUT, ASK ME. IF YOU DON'T LIKE IT, MOVE.