[BioC] getEnrichedGo in ChIPPeakAnno Error
Zhu, Lihua (Julie)
Julie.Zhu at umassmed.edu
Wed May 18 15:46:54 CEST 2011
Gillian,
I think the top six features you selected does not have any corresponding GO
terms assigned. I tried with a few Ensemble IDs from your list, it worked
fine. So I believe if you use the entire annotated dataset, it would work.
enriched.GO =
getEnrichedGO(c("ENSMUSG00000019852","ENSMUSG00000019850","ENSMUSG0000002606
8","ENSMUSG00000026048"), orgAnn="org.Mm.eg.db", maxP=0.01, multiAdj=FALSE,
minGOterm=10, multiAdjMethod="")
Please let me know if it works with the entire dataset. Thanks!
Best regards,
Julie
On 5/18/11 6:33 AM, "Gillian Bob" <gillianscience at yahoo.co.uk> wrote:
> Hi all,
>
> I'm having some trouble with the getEnrichedGo function in ChIPPeakAnno - I
> haven't been able to find a solution by looking through the mailing list, but
> I might not have the right search terms.
>
> With this command:
>
>> SicerGO <- getEnrichedGO(annotatedSicer[1:6,], orgAnn="org.Mm.eg.db",
>> feature_id_type="ensembl_gene_id", maxP=0.01, multiAdj=FALSE, minGOterm=10,
>> multiAdjMethod="")
>
>
> I get the error:
>
>> Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { :
> argument is of length zero
>
> My annotated dataset was generated by using:
>
>> SicerRF = BED2RangedData(SicerDF)
>
> followed by:
>> mart = useMart("ensembl", dataset="mmusculus_gene_ensembl")
>
>> annotatedSicer = annotatePeakInBatch(SicerRF, mart, featureType=c("TSS"))
>> library(org.Mm.eg.db)
>
> and then the Gotest:
>
>> SicerGO <- getEnrichedGO(annotatedSicer[1:6,], orgAnn="org.Mm.eg.db",
>> feature_id_type="ensembl_gene_id", maxP=0.01, multiAdj=FALSE, minGOterm=10,
>> multiAdjMethod="")
>
>
>
> I'm using R version 2.13.0 on Ubuntu.
>
> I'm sure it's something simple, as it works fine on a test dataset. The two
> started off in exactly the same format (chr start stop name number_of_tags)
> and I treated them exactly the same way. As far as I can see, the two
> annotated datasets look exactly the
> same. The error also looks more to do with the go ids than with the datasets
> (though I may be misunderstanding it) - I got the exact same error when I
> accidentally used the human go terms (i.e. orgAnn="org.Hs.eg.db") with my
> mouse data.
>
> This is what my annotated dataset which does not work looks like:
>> annotatedSicer
> RangedData with 89375 rows and 9 value columns across 21 spaces
> space ranges | peak
>
> <factor> <IRanges> | <character>
> peak10 ENSMUSG00000064376 1 [ 4549800, 4551799] | peak10
> peak1002 ENSMUSG00000079587 1 [42968000, 42969199] | peak1002
> peak1003 ENSMUSG00000079587 1 [43009400, 43010599] | peak1003
> peak1004 ENSMUSG00000041878 1 [43148400, 43150199] | peak1004
> peak1008 ENSMUSG00000067579 1 [43321400, 43322199] | peak1008
> peak1009 ENSMUSG00000067579 1 [43340200,
> 43341799] | peak1009
> peak1010 ENSMUSG00000066877 1 [43502000, 43504199] | peak1010
> peak1011 ENSMUSG00000066877 1 [43627600, 43628799] | peak1011
> peak1012 ENSMUSG00000026051 1 [43787400, 43788199] | peak1012
> ... ... ... ... ...
> peak89374 ENSMUSG00000091571 Y [1835800, 1836599] |
> peak89374
> peak89375 ENSMUSG00000090600 Y [2531000, 2531999] | peak89375
> peak89366 ENSMUSG00000053211 Y [ 88800, 89399] | peak89366
> peak89367 ENSMUSG00000075874 Y [ 335000, 335999] | peak89367
> peak89369 ENSMUSG00000068457 Y [ 581200, 582199] | peak89369
> peak89370 ENSMUSG00000069044 Y [ 816800, 817599] | peak89370
> peak89371 ENSMUSG00000069044 Y [ 897000, 897999] | peak89371
> peak89372
> ENSMUSG00000069044 Y [1108800, 1109799] | peak89372
> peak89373 ENSMUSG00000000103 Y [1459800, 1460399] | peak89373
> strand feature start_position
> <character> <character> <numeric>
> peak10
> ENSMUSG00000064376 + ENSMUSG00000064376 4519098
> peak1002 ENSMUSG00000079587 + ENSMUSG00000079587 43009719
> peak1003 ENSMUSG00000079587 + ENSMUSG00000079587 43009719
> peak1004 ENSMUSG00000041878 + ENSMUSG00000041878 43149433
> peak1008 ENSMUSG00000067579 + ENSMUSG00000067579 43246001
> peak1009 ENSMUSG00000067579 +
> ENSMUSG00000067579 43246001
> peak1010 ENSMUSG00000066877 + ENSMUSG00000066877 43502596
> peak1011 ENSMUSG00000066877 + ENSMUSG00000066877 43502596
> peak1012 ENSMUSG00000026051 + ENSMUSG00000026051 43787447
> ... ... ... ...
> peak89374
> ENSMUSG00000091571 + ENSMUSG00000091571 1855009
> peak89375 ENSMUSG00000090600 + ENSMUSG00000090600 2550262
> peak89366 ENSMUSG00000053211 - ENSMUSG00000053211 61650
> peak89367 ENSMUSG00000075874 - ENSMUSG00000075874 328073
> peak89369 ENSMUSG00000068457 - ENSMUSG00000068457 433304
> peak89370 ENSMUSG00000069044 -
> ENSMUSG00000069044 635400
> peak89371 ENSMUSG00000069044 - ENSMUSG00000069044 635400
> peak89372 ENSMUSG00000069044 - ENSMUSG00000069044 635400
> peak89373 ENSMUSG00000000103 - ENSMUSG00000000103 1362123
> end_position insideFeature
> distancetoFeature
> <numeric> <character> <numeric>
> peak10 ENSMUSG00000064376 4519204 downstream 30702
> peak1002 ENSMUSG00000079587 43011992 upstream -41719
> peak1003 ENSMUSG00000079587 43011992 overlapStart -319
> peak1004 ENSMUSG00000041878 43150680
> overlapStart -1033
> peak1008 ENSMUSG00000067579 43246483 downstream 75399
> peak1009 ENSMUSG00000067579 43246483 downstream 94199
> peak1010 ENSMUSG00000066877 43627360 overlapStart -596
> peak1011 ENSMUSG00000066877 43627360 downstream 125004
> peak1012 ENSMUSG00000026051 43799423 overlapStart
> -47
> ... ... ... ...
> peak89374 ENSMUSG00000091571 1855344 upstream -19209
> peak89375 ENSMUSG00000090600 2552957 upstream -19262
> peak89366 ENSMUSG00000053211 133852 inside 45052
> peak89367
> ENSMUSG00000075874 328191 upstream -6809
> peak89369 ENSMUSG00000068457 582202 inside 1002
> peak89370 ENSMUSG00000069044 796225 upstream -20575
> peak89371 ENSMUSG00000069044 796225 upstream -100775
> peak89372 ENSMUSG00000069044 796225 upstream -312575
> peak89373
> ENSMUSG00000000103 1426357 upstream -33443
> shortestDistance fromOverlappingOrNearest
> <numeric> <character>
> peak10 ENSMUSG00000064376 30596 NearestStart
> peak1002
> ENSMUSG00000079587 40520 NearestStart
> peak1003 ENSMUSG00000079587 319 NearestStart
> peak1004 ENSMUSG00000041878 481 NearestStart
> peak1008 ENSMUSG00000067579 74917 NearestStart
> peak1009 ENSMUSG00000067579 93717
> NearestStart
> peak1010 ENSMUSG00000066877 596 NearestStart
> peak1011 ENSMUSG00000066877 240 NearestStart
> peak1012 ENSMUSG00000026051 47 NearestStart
> ...
> ... ...
> peak89374 ENSMUSG00000091571 18410 NearestStart
> peak89375 ENSMUSG00000090600 18263 NearestStart
> peak89366 ENSMUSG00000053211 27150 NearestStart
> peak89367 ENSMUSG00000075874 6809 NearestStart
> peak89369
> ENSMUSG00000068457 3 NearestStart
> peak89370 ENSMUSG00000069044 20575 NearestStart
> peak89371 ENSMUSG00000069044 100775 NearestStart
> peak89372 ENSMUSG00000069044 312575 NearestStart
> peak89373 ENSMUSG00000000103 33443 NearestStart
>
> And this is the
> one which does work:
>> annotatedTest
> RangedData with 6076 rows and 9 value columns across 2 spaces
> space ranges |
> <factor> <IRanges> |
> MACS_peak_1000 ENSMUSG00000070942 1 [40382990, 40382991] |
> MACS_peak_1001 ENSMUSG00000070942 1 [40415507,
> 40415508] |
> MACS_peak_1002 ENSMUSG00000070942 1 [40421610, 40421611] |
> MACS_peak_1003 ENSMUSG00000026068 1 [40603971, 40603972] |
> MACS_peak_1005 ENSMUSG00000079588 1 [41187605, 41187606] |
> MACS_peak_1006 ENSMUSG00000079588 1 [41190193, 41190194] |
> MACS_peak_1007 ENSMUSG00000079588 1 [41196105, 41196106] |
> MACS_peak_1008 ENSMUSG00000079588 1 [41214348, 41214349] |
> MACS_peak_1009 ENSMUSG00000053640 1 [42114801, 42114802]
> |
> ... ... ... ...
> MACS_peak_6057 ENSMUSG00000019853 10 [18355569, 18355570] |
> MACS_peak_6058 ENSMUSG00000019852 10 [18382781, 18382782] |
> MACS_peak_6059 ENSMUSG00000019852 10 [18463508, 18463509] |
> MACS_peak_6064 ENSMUSG00000019850 10 [18734845, 18734846] |
> MACS_peak_6065 ENSMUSG00000019850 10 [18843883, 18843884] |
> MACS_peak_6066 ENSMUSG00000019850 10
> [18873528, 18873529] |
> MACS_peak_6067 ENSMUSG00000019850 10 [18886027, 18886028] |
> MACS_peak_6068 ENSMUSG00000019850 10 [18888316, 18888317] |
> MACS_peak_6069 ENSMUSG00000019850 10 [18897274, 18897275] |
> peak strand
> feature
>
> <character> <character> <character>
> MACS_peak_1000 ENSMUSG00000070942 MACS_peak_1000 +
> ENSMUSG00000070942
> MACS_peak_1001 ENSMUSG00000070942 MACS_peak_1001 +
> ENSMUSG00000070942
> MACS_peak_1002 ENSMUSG00000070942 MACS_peak_1002 +
> ENSMUSG00000070942
> MACS_peak_1003 ENSMUSG00000026068 MACS_peak_1003 +
> ENSMUSG00000026068
> MACS_peak_1005 ENSMUSG00000079588 MACS_peak_1005 +
> ENSMUSG00000079588
> MACS_peak_1006 ENSMUSG00000079588 MACS_peak_1006 +
> ENSMUSG00000079588
> MACS_peak_1007 ENSMUSG00000079588
> MACS_peak_1007 + ENSMUSG00000079588
> MACS_peak_1008 ENSMUSG00000079588 MACS_peak_1008 +
> ENSMUSG00000079588
> MACS_peak_1009 ENSMUSG00000053640 MACS_peak_1009 +
> ENSMUSG00000053640
> ... ... ...
> ...
> MACS_peak_6057 ENSMUSG00000019853 MACS_peak_6057 -
> ENSMUSG00000019853
> MACS_peak_6058 ENSMUSG00000019852
> MACS_peak_6058 - ENSMUSG00000019852
> MACS_peak_6059 ENSMUSG00000019852 MACS_peak_6059 -
> ENSMUSG00000019852
> MACS_peak_6064 ENSMUSG00000019850 MACS_peak_6064 -
> ENSMUSG00000019850
> MACS_peak_6065 ENSMUSG00000019850 MACS_peak_6065 -
> ENSMUSG00000019850
> MACS_peak_6066 ENSMUSG00000019850 MACS_peak_6066 -
> ENSMUSG00000019850
> MACS_peak_6067 ENSMUSG00000019850 MACS_peak_6067 -
> ENSMUSG00000019850
> MACS_peak_6068 ENSMUSG00000019850 MACS_peak_6068 -
> ENSMUSG00000019850
> MACS_peak_6069 ENSMUSG00000019850
> MACS_peak_6069 - ENSMUSG00000019850
> start_position end_position insideFeature
> <numeric> <numeric> <character>
> MACS_peak_1000 ENSMUSG00000070942 40381472 40422316 inside
> MACS_peak_1001 ENSMUSG00000070942 40381472
> 40422316 inside
> MACS_peak_1002 ENSMUSG00000070942 40381472 40422316 inside
> MACS_peak_1003 ENSMUSG00000026068 40572207 40608550 inside
> MACS_peak_1005 ENSMUSG00000079588 40862446 40912112 downstream
> MACS_peak_1006 ENSMUSG00000079588 40862446 40912112 downstream
> MACS_peak_1007 ENSMUSG00000079588 40862446 40912112 downstream
> MACS_peak_1008 ENSMUSG00000079588 40862446 40912112
> downstream
> MACS_peak_1009 ENSMUSG00000053640 42286571 42287953 upstream
> ... ... ... ...
> MACS_peak_6057 ENSMUSG00000019853 18259929 18265882 upstream
> MACS_peak_6058 ENSMUSG00000019852 18307817 18463564 inside
> MACS_peak_6059 ENSMUSG00000019852 18307817
> 18463564 inside
> MACS_peak_6064 ENSMUSG00000019850 18720716 18735463 inside
> MACS_peak_6065 ENSMUSG00000019850 18720716 18735463 upstream
> MACS_peak_6066 ENSMUSG00000019850 18720716 18735463 upstream
> MACS_peak_6067 ENSMUSG00000019850 18720716 18735463 upstream
> MACS_peak_6068 ENSMUSG00000019850 18720716 18735463 upstream
> MACS_peak_6069 ENSMUSG00000019850 18720716
> 18735463 upstream
> distancetoFeature shortestDistance
> <numeric> <numeric>
> MACS_peak_1000 ENSMUSG00000070942 1518 1518
> MACS_peak_1001 ENSMUSG00000070942
> 34035 6808
> MACS_peak_1002 ENSMUSG00000070942 40138 705
> MACS_peak_1003 ENSMUSG00000026068 31764 4578
> MACS_peak_1005 ENSMUSG00000079588 325159 275493
> MACS_peak_1006 ENSMUSG00000079588 327747 278081
> MACS_peak_1007 ENSMUSG00000079588
> 333659 283993
> MACS_peak_1008 ENSMUSG00000079588 351902 302236
> MACS_peak_1009 ENSMUSG00000053640 -171770 171769
> ... ... ...
> MACS_peak_6057 ENSMUSG00000019853 -89687
> 89687
> MACS_peak_6058 ENSMUSG00000019852 80783 74964
> MACS_peak_6059 ENSMUSG00000019852 56 55
> MACS_peak_6064 ENSMUSG00000019850 618 617
> MACS_peak_6065 ENSMUSG00000019850 -108420 108420
> MACS_peak_6066 ENSMUSG00000019850 -138065
> 138065
> MACS_peak_6067 ENSMUSG00000019850 -150564 150564
> MACS_peak_6068 ENSMUSG00000019850 -152853 152853
> MACS_peak_6069 ENSMUSG00000019850 -161811 161811
>
> fromOverlappingOrNearest
> <character>
> MACS_peak_1000 ENSMUSG00000070942 NearestStart
> MACS_peak_1001 ENSMUSG00000070942 NearestStart
> MACS_peak_1002 ENSMUSG00000070942 NearestStart
> MACS_peak_1003 ENSMUSG00000026068 NearestStart
> MACS_peak_1005 ENSMUSG00000079588 NearestStart
> MACS_peak_1006
> ENSMUSG00000079588 NearestStart
> MACS_peak_1007 ENSMUSG00000079588 NearestStart
> MACS_peak_1008 ENSMUSG00000079588 NearestStart
> MACS_peak_1009 ENSMUSG00000053640 NearestStart
> ... ...
> MACS_peak_6057 ENSMUSG00000019853 NearestStart
> MACS_peak_6058
> ENSMUSG00000019852 NearestStart
> MACS_peak_6059 ENSMUSG00000019852 NearestStart
> MACS_peak_6064 ENSMUSG00000019850 NearestStart
> MACS_peak_6065 ENSMUSG00000019850 NearestStart
> MACS_peak_6066 ENSMUSG00000019850 NearestStart
> MACS_peak_6067 ENSMUSG00000019850 NearestStart
> MACS_peak_6068 ENSMUSG00000019850 NearestStart
> MACS_peak_6069 ENSMUSG00000019850
> NearestStart
>
> I tried rebooting R and reinstalling all the packages, and I still end with
> the exact same error. I'm totally stuck and would be really grateful for any
> help.
>
> Thanks!
>
> --Gillian
>
>
>
> [[alternative HTML version deleted]]
>
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