[BioC] How to load annotations for pkgENTREZID, pkgGENENAME dynamically?

[Martin Morgan]

Hi Saurin --

> library(annotate)
> map <- getAnnMap("GENENAME", "hgu95av2")

This will 'do the right thing', e.g., using hgu95av2.db if available,
in preference to hgu95av2.

> probes <- head(ls(map))
> probes
[1] "1000_at"   "1001_at"   "1002_f_at" "1003_s_at" "1004_at"   "1005_at"  
> mget(probes, map)
$`1000_at`
[1] "mitogen-activated protein kinase 3"

$`1001_at`
[1] "tyrosine kinase with immunoglobulin-like and EGF-like domains 1"

$`1002_f_at`
[1] "cytochrome P450, family 2, subfamily C, polypeptide 19"

$`1003_s_at`
[1] "chemokine (C-X-C motif) receptor 5"

$`1004_at`
[1] "chemokine (C-X-C motif) receptor 5"

$`1005_at`
[1] "dual specificity phosphatase 1"

which works on both environment and .db packages.

Martin

"Jani, Saurin D" <jani at musc.edu> writes:

> Dear BioC,
>
> Here is my R script code which is running on  server in background.
> ##################################
> chiptype <- annotation(affy_batch_object);
>
> if(chiptype == "hu6800")
> {
> library(hu6800cdf);
> library(hu6800probe);
> library(hu6800);
> library(humanCHRLOC);
> library(humanLLMappings);
> envGeneNames <- hu6800GENENAME; # very important
> envPath2Probes <- hu6800PATH2PROBE;
> envGO2AllPROBES <- hu6800GO2ALLPROBES;
> envGENEIDS <- hu6800ENTREZID; # very important
> }
>
> and so on for commonly used AFFY Chips....
> ##################################
>
> I have written this manually, how can I load annotations and
> packageENGREZID, packageGENENAME..etc. dynamically?
>
> I am currently working with Affy chips but I also like to work on
> Agilent chips in futureI.
>
> OR
>
> I just write a perl/php scripts which prints above information...thats my thinking.
>
> Thank you so much in advance,
> Saurin
>
>
> |------------------------------------------------
> | Saurin D. Jani
> | Bioinformatician
> |
> | Department of Cell Biology and Anatomy
> | Medical  University of South Carolina (MUSC)
> | 173 Ashley Ave
> | Charleston,SC - 29425
> |
> | Email: jani at musc.edu
> | Phone: (843)792-1340
> | Website: http://www.musc.edu/~jani
> |------------------------------------------------
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793