How to load annotations for pkgENTREZID, pkgGENENAME dynamically?
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@martin-morgan-1513
Last seen 6 days ago
United States
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 > |------------------------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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
Cancer hgu95av2 affy Cancer hgu95av2 affy • 496 views
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@saurin-d-jani-944
Last seen 7.4 years ago
Hi there, thanks, Sean and Matin....now it works fantastic....!! 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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