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Gillian Bob
▴
20
@gillian-bob-4650
Last seen 10.5 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
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