Entering edit mode
Aayush,
The getEnrichedGO expects annotatedPeak as a RangedData returned from
annotatePeakInBatch which contains a field feature, or a character
vector containing the feature IDs. Supported feature ID types are
ensembl_gene_id, refseq_id, gene_symbol and entrez_id.
So for your dataset, you could extract the gene symbols or ensembl
IDs. Alternatively, you could change names.ensembl_gene_id to feature.
Best regards,
Julie
On 7/13/11 9:15 PM, "Ayush Raman" <ayush.raman@systemsbiology.org>
wrote:
Hi Julie,
I hope you are doing good. I am trying to do the GO enrichment on a
RangedData object. I am running the following command:
enrichedGO = getEnrichedGO(m.RangedData, orgAnn="org.Mm.eg.db", maxP=
0.01, multiAdj = TRUE, minGOterm = 10, multiAdjMethod="BH")
my m.RangedData object looks like:
RangedData with 236 rows and 11 value columns across 202 spaces
space ranges |
names.ensembl_gene_id names.RefSeqIds names.Entrez.ID
<http: names.entrez.id=""> names.Gene.Symbol
<character> <iranges> |
<character> <factor> <factor> <factor>
1 ENSMUSG00000000489 [ 79826330, 79845238] |
ENSMUSG00000000489 NM_011057 18591 Pdgfb
2 ENSMUSG00000000740 [125626250, 125629144] |
ENSMUSG00000000740 NM_016738 270106 Rpl13
3 ENSMUSG00000001123 [ 78776476, 78798448] |
ENSMUSG00000001123 NM_001159301 16859 Lgals9
4 ENSMUSG00000001123 [ 78776476, 78798448] |
ENSMUSG00000001123 NM_010708 16859 Lgals9
5 ENSMUSG00000002699 [ 33946920, 33992295] |
ENSMUSG00000002699 NM_010696 16822 Lcp2
6 ENSMUSG00000003135 [ 39591837, 39603726] |
ENSMUSG00000003135 NM_028043 52846 D1Bwg0212e
7 ENSMUSG00000003283 [152934204, 152977177] |
ENSMUSG00000003283 NM_001172117 15162 Hck
8 ENSMUSG00000003283 [152934204, 152977177] |
ENSMUSG00000003283 NM_010407 15162 Hck
9 ENSMUSG00000003437 [ 29177970, 29184407] |
ENSMUSG00000003437 NM_019458 54624 Paf1
... ... ... ...
... ... ... ...
228 ENSMUSG00000074218 [ 30969190, 30971047] |
ENSMUSG00000074218 NM_009944 12865 Cox7a1
229 ENSMUSG00000074922 [ 24550992, 24551846] |
ENSMUSG00000074922 NM_026520 68034 Fam122a
230 ENSMUSG00000078201 [ 25110959, 25111872] |
ENSMUSG00000078201 NM_177344 227615 Tmem203
231 ENSMUSG00000079197 [ 56206278, 56209950] |
ENSMUSG00000079197 NM_001029855 19188 Psme2
232 ENSMUSG00000079197 [ 56206278, 56209950] |
ENSMUSG00000079197 NM_011190 19188 Psme2
233 ENSMUSG00000079252 [157882856, 157900866] |
ENSMUSG00000079252 NM_001160181 240832 Tor1aip2
234 ENSMUSG00000079252 [157882856, 157900866] |
ENSMUSG00000079252 NM_022329 240832 Tor1aip2
235 ENSMUSG00000079737 [ 13672022, 13678498] |
ENSMUSG00000079737 NM_025653 66598 3110001I22Rik
236 ENSMUSG00000089944 [ 55392211, 55392727] |
ENSMUSG00000089944 NM_207635 20088 Rps24
names.OnThreePrimeArray names.DiffExp names.Score
names.Other.Gene.Near names.chromosome_name names.start_position
<factor> <factor> <factor>
<factor> <character> <integer>
1 1 0 10.581459
0 15 79826330
2 0 0 13.226824
0 8 125626250
3 1 1 4.534911
0 11 78776476
4 1 1 4.534911
0 11 78776476
5 1 1 2.645365
0 11 33946920
6 1 0 2.645365
0 1 39591837
7 1 1 2.645365
0 2 152934204
8 1 1 2.645365
0 2 152934204
9 1 0 6.046548
1 7 29177970
... ... ... ...
... ... ...
228 1 0 3.023274
1 7 30969190
229 1 0 5.668639
1 19 24550992
230 1 0 3.779092
1 2 25110959
231 0 0 2.645365
1 14 56206278
232 0 0 2.645365
1 14 56206278
233 1 1 3.023274
0 1 157882856
234 1 1 3.023274
0 1 157882856
235 1 1 4.91282
1 16 13672022
236 0 0 7.936094
0 1 55392211
names.end_position
<integer>
1 79845238
2 125629144
3 78798448
4 78798448
5 33992295
6 39603726
7 152977177
8 152977177
9 29184407
... ...
228 30971047
229 24551846
230 25111872
231 56209950
232 56209950
233 157900866
234 157900866
235 13678498
236 55392727
Actually I processed bed file and didn't used Annotatedpeak function
from ChIPpeakAnno. I performed certain functions got the table as a
RangedData object.
Now, I am getting a following error after running the getEnrichedGO
command:
Error in if (class(go.ids) != "matrix" | dim(go.ids)[2] < 4) { :
argument is of length zero
In addition: Warning message:
In is.na <http: is.na=""> (IDs) : is.na <http: is.na=""> () applied to
non-(list or vector) of type 'NULL'
My session info is as follows:
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] RColorBrewer_1.0-2 ChIPpeakAnno_1.6.0
limma_3.6.9
[4] org.Hs.eg.db_2.4.6 GO.db_2.4.5
BSgenome.Ecoli.NCBI.20080805_1.3.16
[7] BSgenome_1.18.3 GenomicRanges_1.2.3
Biostrings_2.18.4
[10] IRanges_1.8.9 multtest_2.7.1
org.Mm.eg.db_2.4.6
[13] RSQLite_0.9-4 DBI_0.2-5
AnnotationDbi_1.12.0
[16] Biobase_2.10.0 biomaRt_2.6.0
loaded via a namespace (and not attached):
[1] MASS_7.3-11 RCurl_1.4-3 splines_2.12.0 survival_2.36-5
tools_2.12.0 XML_3.2-0
Please let me know where I am going wrong to correct this error. Any
advice/hints will be highly appreciated.
Thanks.
Aayush Raman
Bioinformatics Research Scientist
Institute for Systems Biology
Seattle WA
206-732-1473
[[alternative HTML version deleted]]