[BioC] AnnotationDbi quesion please help

[David Lyon]

OK it looks like its mapping on the opposite strand so its '-'
ignore my last question

thanks for your help vincent and everyone, I should be able to take it from here.



----- Original Message ----
From: David Lyon <david_lyon3 at yahoo.com>
To: Vincent Carey <stvjc at channing.harvard.edu>
Cc: bioconductor at stat.math.ethz.ch
Sent: Tue, May 18, 2010 8:35:42 PM
Subject: Re: [BioC] AnnotationDbi quesion please help

Thanks I should be able to script it from here

does anyone know what the following results mean?

> toTable(hugene10sttranscriptclusterCHRLOCEND) [1:7, ]
  probe_id end_location Chromosome
1  8039748    -63556677         19
2  7960947     -9159825         12
3  8144857     18125477          8
4  8144857     18125477          8
5  8144857     18125477          8
6  8144866     18303003          8



how can there be negative coordinates?







________________________________
From: Vincent Carey <stvjc at channing.harvard.edu>

Cc: bioconductor at stat.math.ethz.ch
Sent: Tue, May 18, 2010 7:46:50 PM
Subject: Re: [BioC] AnnotationDbi quesion please help

is this a reasonable example of what you want?

> toTable(hugene10sttranscriptclusterENSEMBL)[1:4,]
  probe_id      ensembl_id
1  8039748 ENSG00000121410
2  7960947 ENSG00000175899
3  8144857 ENSG00000171428
4  8144866 ENSG00000156006





>How do I get to output the mapped keys for the all of the following "head(qcdata, 50)"
>
>>eg : output the keys and values for "hugene10sttranscriptclusterENSEMBL has 20276 mapped keys (of 33297 keys)"
>>and all the others
>
>>Thanks for your help
>
>
>
>
>>> qcdata=capture.output(hugene10sttranscriptcluster())
>>> head(qcdata, 50)
>> [1] "Quality control information for hugene10sttranscriptcluster:"
>> [2] ""
>> [3] ""
>> [4] "This package has the following mappings:"
>> [5] ""
>> [6] "hugene10sttranscriptclusterACCNUM has 32969 mapped keys (of 33297 keys)"
>> [7] "hugene10sttranscriptclusterALIAS2PROBE has 74639 mapped keys (of 109070 keys)"
>> [8] "hugene10sttranscriptclusterCHR has 21890 mapped keys (of 33297 keys)"
>> [9] "hugene10sttranscriptclusterCHRLENGTHS has 25 mapped keys (of 25 keys)"
>>[10] "hugene10sttranscriptclusterCHRLOC has 21134 mapped keys (of 33297 keys)"
>>[11] "hugene10sttranscriptclusterCHRLOCEND has 21134 mapped keys (of 33297 keys)"
>>[12] "hugene10sttranscriptclusterENSEMBL has 20276 mapped keys (of 33297 keys)"
>>[13] "hugene10sttranscriptclusterENSEMBL2PROBE has 18678 mapped keys (of 19892 keys)"
>>[14] "hugene10sttranscriptclusterENTREZID has 21891 mapped keys (of 33297 keys)"
>>[15] "hugene10sttranscriptclusterENZYME has 2165 mapped keys (of 33297 keys)"
>>[16] "hugene10sttranscriptclusterENZYME2PROBE has 900 mapped keys (of 901 keys)"
>>[17] "hugene10sttranscriptclusterGENENAME has 21891 mapped keys (of 33297 keys)"
>>[18] "hugene10sttranscriptclusterGO has 18441 mapped keys (of 33297 keys)"
>>[19] "hugene10sttranscriptclusterGO2ALLPROBES has 11220 mapped keys (of 11236 keys)"
>>[20] "hugene10sttranscriptclusterGO2PROBE has 8224 mapped keys (of 8245 keys)"
>>[21] "hugene10sttranscriptclusterMAP has 21809 mapped keys (of 33297 keys)"
>>[22] "hugene10sttranscriptclusterOMIM has 13697 mapped keys (of 33297 keys)"
>>[23] "hugene10sttranscriptclusterPATH has 5447 mapped keys (of 33297 keys)"
>>[24] "hugene10sttranscriptclusterPATH2PROBE has 220 mapped keys (of 220 keys)"
>>[25] "hugene10sttranscriptclusterPFAM has 21342 mapped keys (of 33297 keys)"
>>[26] "hugene10sttranscriptclusterPMID has 21451 mapped keys (of 33297 keys)"
>>[27] "hugene10sttranscriptclusterPMID2PROBE has 244607 mapped keys (of 248847 keys)"
>>[28] "hugene10sttranscriptclusterPROSITE has 21342 mapped keys (of 33297 keys)"
>>[29] "hugene10sttranscriptclusterREFSEQ has 21721 mapped keys (of 33297 keys)"
>>[30] "hugene10sttranscriptclusterSYMBOL has 21891 mapped keys (of 33297 keys)"
>>[31] "hugene10sttranscriptclusterUNIGENE has 21474 mapped keys (of 33297 keys)"
>>[32] "hugene10sttranscriptclusterUNIPROT has 20875 mapped keys (of 33297 keys)"
>>[33] ""
>>[34] ""
>>[35] "Additional Information about this package:"
>>[36] ""
>>[37] "DB schema: HUMANCHIP_DB"
>>[38] "DB schema version: 2.0"
>>[39] "Organism: Homo sapiens"
>>[40] "Date for NCBI data: 2009-Sep1"
>>[41] "Date for GO data: 20090830"
>>[42] "Date for KEGG data: 2009-Sep16"
>>[43] "Date for Golden Path data: 2009-Jul5"
>>[44] "Date for IPI data: 2009-Jul29"
>>[45] "Date for Ensembl data: 2009-Jul14"
>
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