getEnrichedGo in ChIPPeakAnno Error
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Gillian Bob ▴ 20
@gillian-bob-4650
Last seen 9.6 years ago
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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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 5 months ago
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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","ENSMUSG0000 002606 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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Hi, Yes, it's working now!  I was misunderstanding the purpose of the [1:6,] - I thought it meant columns and not rows - didn't realise I was selecting out the top six! Thanks very much for your help. --Gillian --- On Wed, 18/5/11, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: From: Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> Subject: Re: [BioC] getEnrichedGo in ChIPPeakAnno Error To: "Gillian Bob" <gillianscience@yahoo.co.uk>, "bioconductor@r-project.org" <bioconductor@r-project.org> Date: Wednesday, 18 May, 2011, 13:46 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","ENSMUSG0000 002606 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@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]] > [[alternative HTML version deleted]]
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