[BioC] Question RE: getEnrichedGo in ChIPpeakAnno package

[Noah Dowell]

Hello All,

I couldn't find a solution to my question in the archives and my attempts have been unsuccessful so hopefully someone has some advice.

I have analyzed my yeast ChIP-chip tiling array data using Starr and converted my list of chip-enriched regions to RangedData to make use of the peakOverlap and GOenrichment functions in ChIPpeakAnno.  The annotatePeakInBatch function has worked nicely but I am stuck with the getEnrichedGO function.  I think the problem may be due to differences between the org.Hs.eg.db and org.Sc.sgd.db.  The org.Hs.eg.db has a mapping of ENSEMBL gene accession numbers to Entrez Gene identifiers, but the org.Sc.sgd.db completely lacks this and uses a mapping to SGD Gene Identifiers.  As far as I can tell the getEnrichedGO function calls for a mapping to Entrez Gene ids thus the error I am showing below.  

Does anyone know of a work around for this?

Thank you for your help.

Noah


>library(org.Sc.sgd.db)

> goTest <- getEnrichedGO(annoPeakChr1data, orgAnn = "org.Sc.sgd.db", maxP = 0.01, multiAdj =TRUE, minGOterm = 10, multiAdjMethod = "BH")
Error in get(paste(GOgenome, "ENSEMBL2EG", sep = "")) : 
  object 'org.Sc.sgdENSEMBL2EG' not found

##also tried:

> goTest <- getEnrichedGO(annoPeakChr1data, orgAnn = "org.Sc.sgd.db", feature_id_type= "ensembl_gene_id", maxP = 0.01, multiAdj =TRUE, minGOterm = 10, multiAdjMethod = "BH")
Error in get(paste(GOgenome, "ENSEMBL2EG", sep = "")) : 
  object 'org.Sc.sgdENSEMBL2EG' not found

#### here is what my annotatePeak Object looks like:

> head(annoPeakChr1data)
RangedData with 6 rows and 9 value columns across 1 space
                   space         ranges |        peak      strand     feature start_position end_position
             <character>      <IRanges> | <character> <character> <character>      <numeric>    <numeric>
01 YAL069W             I [   16,   254] |          01           1     YAL069W            335          649
02 YAL067W-A           I [ 2731,  2924] |          02           1   YAL067W-A           2480         2707
06 YAL062W             I [29935, 29959] |          06           1     YAL062W          31568        32941
07 YAL062W             I [30011, 30039] |          07           1     YAL062W          31568        32941
08 YAL062W             I [31661, 31678] |          08           1     YAL062W          31568        32941
09 YAL062W             I [31702, 31710] |          09           1     YAL062W          31568        32941









> sessionInfo()
R version 2.11.0 (2010-04-22) 
i386-apple-darwin9.8.0 

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] org.Sc.sgd.db_2.4.1                 rtracklayer_1.8.1                   RCurl_1.3-1                         bitops_1.0-4.1                     
 [5] Starr_1.4.0                         affxparser_1.20.0                   affy_1.26.0                         Ringo_1.12.0                       
 [9] Matrix_0.999375-38                  lattice_0.18-5                      RColorBrewer_1.0-2                  ChIPpeakAnno_1.4.0                 
[13] limma_3.4.0                         org.Hs.eg.db_2.4.1                  GO.db_2.4.1                         RSQLite_0.8-4                      
[17] DBI_0.2-5                           AnnotationDbi_1.10.0                BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.16.0                    
[21] GenomicRanges_1.0.1                 Biostrings_2.16.0                   IRanges_1.6.0                       multtest_2.4.0                     
[25] Biobase_2.8.0                       biomaRt_2.4.0                      

loaded via a namespace (and not attached):
 [1] affyio_1.16.0         annotate_1.26.0       genefilter_1.30.0     MASS_7.3-5            preprocessCore_1.10.0 pspline_1.0-14       
 [7] splines_2.11.0        survival_2.35-8       tools_2.11.0          XML_2.8-1             xtable_1.5-6