[BioC] ChIPpeakAnno::getEnrichedGo crashes but I don't know why
Zhu, Lihua (Julie)
Julie.Zhu at umassmed.edu
Wed Jan 5 19:02:24 CET 2011
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_ensembl
>> ">
>> )
>>> 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=0.01,
>>> 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
>>>
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>>>
>>
>>
>
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