[BioC] ChIPpeakAnno::getEnrichedGo crashes but I don't know why
Eric Cabot
elcabot at gmail.com
Wed Jan 5 23:31:41 CET 2011
Julie,
I don't know how to do that in R. I guess I can always export the
annotations, do the association in Perl and re-import them as a vector to
use with getEnrichedGo.
Eric
Zhu, Lihua (Julie) wrote:
> Eric,
>
> You could convert the exon IDs associated with the peaks to ensemble gene
> IDs and input these ensemble gene IDs to the getEnrichedGO function.
>
> Best regards,
>
> Julie
>
>
> On 1/5/11 4:09 PM, "Eric Cabot" <elcabot at gmail.com> wrote:
>
>> Hi Julie,
>>
>> It may be a while before I get back to you on this, because I did my
>> mapping and ChIP-Seq analysis with Hg19 (NCBI 37), not Hg18 (NCBI 36).
>> I'm also a little concerned about using transcription start site
>> annotations rather than exons, because the the binding domains are not
>> thought to be restricted to only promoters. Any suggestions?
>>
>> Eric
>>
>>
>>
>> Zhu, Lihua (Julie) wrote:
>>> Eric,
>>>
>>> The annotated dataset has exon ID instead of gene ID while the getEnrichedGO
>>> is expecting feature_id_type="ensembl_gene_id". For a list of supported
>>> feature_id_type, please type ?getEnrichedGO.
>>>
>>> To use getEnrichedGO function, first get the TSS annotation.
>>>
>>> TSS.human.NCBI36 = getAnnotation(ENSEMBLE_GENES_MART, featureType="TSS")
>>>
>>> or use the build in TSS as
>>>
>>> data(TSS.human.NCBI36)
>>>
>>> Then annotate your peaks with TSS.human.NCBI36 followed by getEnrichedGO
>>> call.
>>>
>>> Please let me know if this works for you.
>>>
>>> Best regards,
>>>
>>> Julie
>>>
>>>
>>>
>>>
>>> On 1/5/11 12:29 PM, "Eric Cabot" <elcabot at gmail.com> wrote:
>>>
>>>> Hi Julie,
>>>>
>>>> Thank you for your response.
>>>>
>>>> Here is the sessionInfo and traceback output and also a few lines of
>>>> "my_annotated_regions".
>>>>
>>>> Regards,
>>>>
>>>> Eric Cabot
>>>>
>>>>> sessionInfo()
>>>> R version 2.12.1 (2010-12-16)
>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>
>>>> locale:
>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> other attached packages:
>>>> [1] ChIPpeakAnno_1.6.0 limma_3.6.9
>>>> [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5
>>>> [5] RSQLite_0.9-4 DBI_0.2-5
>>>> [7] AnnotationDbi_1.12.0
>>>> BSgenome.Ecoli.NCBI.20080805_1.3.16
>>>> [9] BSgenome_1.18.2 GenomicRanges_1.2.2
>>>> [11] Biostrings_2.18.2 IRanges_1.8.8
>>>> [13] multtest_2.6.0 Biobase_2.10.0
>>>> [15] biomaRt_2.6.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] MASS_7.3-9 RCurl_1.5-0 splines_2.12.1 survival_2.36-2
>>>> [5] tools_2.12.1 XML_3.2-0
>>>> my_enrichedGO<-getEnrichedGO(my_annotated_regions,orgAnn="org.Hs.eg.db",maxP
>>>> =0
>>>> .01,multiAdj=FALSE,minGOterm=1,feature_id_type="ensembl_gene_id")
>>>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { :
>>>> argument is of length zero
>>>>> traceback()
>>>> 2: addAncestors(this.GO[this.GO[, 3] == "BP", ], "bp")
>>>> 1: getEnrichedGO(FC2_annotated_regions, orgAnn = "org.Hs.eg.db",
>>>> maxP = 0.01, multiAdj = FALSE, minGOterm = 1, feature_id_type =
>>>> "ensembl_gene_id")
>>>>
>>>>
>>>>
>>>>> as.data.frame(my_annotated_regions[1:15,])
>>>> space start end width names peak strand
>>>> 1 1 241997936 241998205 270 R-10060 ENSE00001749374 R-10060 +
>>>> 2 1 237109743 237110002 260 R-10082 ENSE00001643382 R-10082 +
>>>> 3 1 236080267 236080415 149 R-10086 ENSE00001807176 R-10086 +
>>>> 4 1 233853245 233853514 270 R-10096 ENSE00001776382 R-10096 +
>>>> 5 1 233727956 233728104 149 R-10097 ENSE00001442190 R-10097 +
>>>> 6 1 230728554 230728823 270 R-10108 ENSE00001731401 R-10108 +
>>>> 7 1 229687129 229687277 149 R-10113 ENSE00001439385 R-10113 +
>>>> 8 1 228943263 228943412 150 R-10121 ENSE00001903546 R-10121 +
>>>> 9 1 218358885 218359176 292 R-10157 ENSE00001439386 R-10157 +
>>>> 10 1 212254259 212254408 150 R-10179 ENSE00001624346 R-10179 +
>>>> 11 1 210086264 210086513 250 R-10184 ENSE00001903225 R-10184 +
>>>> 12 1 209863549 209863698 150 R-10185 ENSE00001336255 R-10185 +
>>>> 13 1 207437117 207437264 148 R-10190 ENSE00001742112 R-10190 +
>>>> 14 1 190352400 190352548 149 R-10246 ENSE00001782518 R-10246 +
>>>> 15 1 184432607 184432755 149 R-10260 ENSE00001283926 R-10260 +
>>>> feature start_position end_position insideFeature
>>>> distancetoFeature
>>>> 1 ENSE00001749374 241995237 241996089 downstream
>>>> 2699
>>>> 2 ENSE00001643382 237144639 237145008 upstream
>>>> -34896
>>>> 3 ENSE00001807176 236078715 236078821 downstream
>>>> 1552
>>>> 4 ENSE00001776382 233807017 233807237 downstream
>>>> 46228
>>>> 5 ENSE00001442190 233749750 233750272 upstream
>>>> -21794
>>>> 6 ENSE00001731401 230728406 230728586 overlapEnd
>>>> 148
>>>> 7 ENSE00001439385 229685652 229685769 downstream
>>>> 1477
>>>> 8 ENSE00001903546 228882063 228882416 downstream
>>>> 61200
>>>> 9 ENSE00001439386 218303137 218303294 downstream
>>>> 55748
>>>> 10 ENSE00001624346 212253973 212254092 downstream
>>>> 286
>>>> 11 ENSE00001903225 210111538 210111622 upstream
>>>> -25274
>>>> 12 ENSE00001336255 209859550 209859630 downstream
>>>> 3999
>>>> 13 ENSE00001742112 207438342 207438381 upstream
>>>> -1225
>>>> 14 ENSE00001782518 190331193 190331400 downstream
>>>> 21207
>>>> 15 ENSE00001283926 184446520 184446737 upstream
>>>> -13913
>>>> shortestDistance fromOverlappingOrNearest
>>>> 1 1847 NearestStart
>>>> 2 34637 NearestStart
>>>> 3 1446 NearestStart
>>>> 4 46008 NearestStart
>>>> 5 21646 NearestStart
>>>> 6 32 NearestStart
>>>> 7 1360 NearestStart
>>>> 8 60847 NearestStart
>>>> 9 55591 NearestStart
>>>> 10 167 NearestStart
>>>> 11 25025 NearestStart
>>>> 12 3919 NearestStart
>>>> 13 1078 NearestStart
>>>> 14 21000 NearestStart
>>>> 15 13765 NearestStart
>>>>
>>>>
>>>> Zhu, Lihua (Julie) wrote:
>>>>> Hi Eric,
>>>>>
>>>>> Could you please post the session information with sessionInfo() command?
>>>>> Could you please also send a few ensembl IDs in your annotated dataset?
>>>>> Thanks!
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Julie
>>>>>
>>>>>
>>>>> On 1/4/11 6:51 PM, "Eric Cabot" <elcabot at gmail.com> wrote:
>>>>>
>>>>>> I am a relatively new Bioconductor user and I am trying to analyze some
>>>>>> ChIP-seq results that came from QuEST using the ChIPpeakAnno package.
>>>>>>
>>>>>> After importing the regions of interest into RangedData objects and doing
>>>>>> the following:
>>>>>>
>>>>>>
>>>>> ENSEMBLE_GENES_MART<-useMart(biomart="ensembl",dataset="hsapiens_gene_ensem
>>>>> bl
>>>>> ">
>>>>> )
>>>>>> ENSEMBL_ExonPlus_Annotation<-getAnnotation(ENSEMBLE_GENES_MART,
>>>>>> featureType="ExonPlusUtr")
>>>>>>
>>>>>>
>>>>>> I had no problem annotating and generating a Venn diagram to show the
>>>>>> overlaps between my three sets of peaks. To annotate, I used:
>>>>>>
>>>>>> annotated_regions=annotatePeakInBatch(myranged,
>>>>>> AnnotationData=ENSEMBL_ExonPlus_Annotation)
>>>>>>
>>>>>>
>>>>>> But I cannot seem to get the getEnrichedGo method to work on this (or my
>>>>>> other two annotated regions). Here is a typical command line:
>>>>>>
>>>>>>
>>>>>> my_enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",maxP=
>>>>>> 0.
>>>>>> 01
>>>>>> ,multiAdj=TRUE,minGOterm=1,
>>>>>> multiAdjMethod="BH",feature_id_type="ensembl_gene_id")
>>>>>>
>>>>>> and here is a typical error message:
>>>>>>
>>>>>> enrichedGO<-getEnrichedGO(annotated_regions,orgAnn="org.Hs.eg.db",maxP=0.0
>>>>>> 1,
>>>>>> mu
>>>>>> ltiAdj=TRUE,minGOterm=1,feature_id_type="ensembl_gene_id")
>>>>>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { :
>>>>>> argument is of length zero
>>>>>>
>>>>>>
>>>>>> Which leads me to ask:
>>>>>>
>>>>>> 1) Is this error message supposed to be meaningful to me-i.e. a user-or is
>>>>>> it something that I should be sending to the developer of the package?
>>>>>>
>>>>>> 2) Is there anything obvious from this that suggests what corrective
>>>>>> action I should be taking?
>>>>>>
>>>>>>
>>>>>> Eric Cabot
>>>>>> University of Wisconsin
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor at r-project.org
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>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>
>>>
>
>
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