[BioC] importing ID table in AnnotationDbi

[Marc Carlson]

Hi Dana,

First of all let me say that it fills me with joy to see someone finally 
making use of the "chicken.db0" package.  Next, I think the error you 
have is trying to indicate that you need to pass "GGal_ID_UG.txt" in to 
the file parameter.  Like this:

populateDB("CHICKENCHIP_DB", affy = FALSE, prefix = "GGal", fileName = 
"GGal_ID_UG.txt", metaDataSrc = myMeta, baseMapType = "ug")

Let me know if you have other problems that crop up.


   Marc




On 03/17/2011 08:33 PM, Dana.Stanley at csiro.au wrote:
> I am trying to make annotation package for my array platform using AnnotationDbi package. I prepared txt file that links customID and unigene. The table I am trying to import here has only 2 columns; one is gene id (CLIGG_00001) and the other is unigene id (Gga.1). I tried all I could google out and many as.character or bimap options...Here is  the R output:
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>> setwd("/home/dana/MICROARRAY/Results/Pancreas")
>> dir()
> [1] "GGal_ID_UG.txt"
>
>
>
>> library(AnnotationDbi)
>
>
>> GGal_ID=read.table(as.character("GGal_ID_UG.txt", sep = "\t", header = FALSE, as.is = TRUE))
>
>
>> mode(GGal_ID)
> [1] "list"
>
>> class(GGal_ID)
> [1] "data.frame"
>
>> #
>> #
>> ls()
> [1] "GGal_ID"
>
>
>
>> head (GGal_ID)
>             V1    V2
>
> 1 CLIGG_00001 Gga.1
>
> 2 CLIGG_00002 Gga.3
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> 3 CLIGG_00003 Gga.4
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> 4 CLIGG_00004 Gga.5
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> 5 CLIGG_00005 Gga.6
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> 6 CLIGG_00006 Gga.6
>
>
>
>> available.db0pkgs()
> [1] "anopheles.db0"   "arabidopsis.db0" "bovine.db0"      "canine.db0"
>
>   [5] "chicken.db0"     "chimp.db0"       "ecoliK12.db0"    "ecoliSakai.db0"
>
>   [9] "fly.db0"         "human.db0"       "malaria.db0"     "mouse.db0"
>
> [13] "pig.db0"         "rat.db0"         "rhesus.db0"      "worm.db0"
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> [17] "xenopus.db0"     "yeast.db0"       "zebrafish.db0"
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>> library(chicken.db0)
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>> myMeta = c("DBSCHEMA"="CHICKENCHIP_DB", "ORGANISM"="Gallus gallus", "SPECIES"="Chicken", "MANUFACTURER"="NimbleGen", "CHIPNAME"="090716_Ggal_RM_EXP", "MANUFACTURERURL"="http://www.roche.com")
>
>
>> populateDB("CHICKENCHIP_DB", affy = FALSE, prefix = "GGal", fileName = GGal_ID, metaDataSrc = myMeta, baseMapType = "ug")
> Error in read.table(file = file, header = header, sep = sep, quote = quote,  :
>
>    'file' must be a character string or connection
>
>
> How to import my table (GGal_ID_UG.txt) as a character string or connection? Is there a simple code to get from my own txt file to a annotation package?
>
> Thanks in advance for posting a reply.
>
> Dana
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