[BioC] AnnBuilder question: about how to retrieve information when using a built package?
Ting-Yuan Liu
tliu at fhcrc.org
Mon Nov 28 18:49:02 CET 2005
Hi Johan,
is.environment() should be helpful. Use ?is.environment for more detail.
HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________
On Thu, 24 Nov 2005, Johan Lindberg wrote:
> Hi. I am writing a function doing home-brewed chromosomal plots but I have
> run in to a problem when I want to make it more general.
>
>
>
> When you load your home-made package created with the help of AnnBuilder
> environments become available with different information.
>
>
>
> ######################################################
>
> ls("package:Hum30kbatch1to5")
>
> [1] "Hum30kbatch1to5"
>
> [2] "Hum30kbatch1to5ACCNUM"
>
> [3] "Hum30kbatch1to5CHR"
>
> [4] "Hum30kbatch1to5CHRLENGTHS"
>
> [5] "Hum30kbatch1to5CHRLOC"
>
> [6] "Hum30kbatch1to5ENZYME"
>
> [7] "Hum30kbatch1to5ENZYME2PROBE"
>
> [8] "Hum30kbatch1to5GENENAME"
>
> [9] "Hum30kbatch1to5GO"
>
> [10] "Hum30kbatch1to5GO2ALLPROBES"
>
> [11] "Hum30kbatch1to5GO2PROBE"
>
> [12] "Hum30kbatch1to5LOCUSID"
>
> [13] "Hum30kbatch1to5MAP"
>
> [14] "Hum30kbatch1to5MAPCOUNTS"
>
> [15] "Hum30kbatch1to5OMIM"
>
> [16] "Hum30kbatch1to5ORGANISM"
>
> [17] "Hum30kbatch1to5PATH"
>
> [18] "Hum30kbatch1to5PATH2PROBE"
>
> [19] "Hum30kbatch1to5PFAM"
>
> [20] "Hum30kbatch1to5PMID"
>
> [21] "Hum30kbatch1to5PMID2PROBE"
>
> [22] "Hum30kbatch1to5PROSITE"
>
> [23] "Hum30kbatch1to5QC"
>
> [24] "Hum30kbatch1to5QCDATA"
>
> [25] "Hum30kbatch1to5REFSEQ"
>
> [26] "Hum30kbatch1to5SUMFUNC"
>
> [27] "Hum30kbatch1to5SYMBOL"
>
> [28] "Hum30kbatch1to5UNIGENE"
>
> ######################################################
>
>
>
> I thought they all were environments and if you want to call an environment
> from within a function you could use something like:
>
>
>
> getEnvironment <- function(chipName, environment)
>
> {
>
> get(paste(chipName, environment, sep = ""), mode =
> "environment")
>
> }
>
>
>
> To prevent having to pass every environment that I want to use in the
> function as an argument.
>
>
>
> But I discovered that the "Hum30kbatch1to5CHRLENGTHS" was a vector rather
> than an environment and that it is accessible from my workspace. If I type
> just
>
>
>
> ###############################################
>
> > Hum30kbatch1to5CHRLENGTHS
>
> 1 2 3 4 5 6
>
> 246127941 243615958 199344050 191731959 181034922 170914576
>
> 7 8 9 10 11 12
>
> 158545518 146308819 136372045 135037215 134482954 132078379
>
> 13 14 15 16 17 18
>
> 113042980 105311216 100256656 90041932 81860266 76115139
>
> 19 20 21 22 X Y
>
> 63811651 63741868 46976097 49396972 153692391 50286555
>
> M
>
> 16571
>
> ###############################################
>
> then I get the lengths of the different chromosomes.
>
>
>
> How do I get hold of this information from within a function if I do not
> want to give the whole object as an argument? I only want to provide the
> name of my package and then get hold of all information. Could one use get?
> But how? I tried something like
>
>
>
> get("Hum30kbatch1to5","CHRLENGTHS", mode = "numeric")
>
> Error in as.environment(pos) : no item called "CHRLENGTHS" on the search
> list
>
>
>
> but that didn't work since it isn't accessible in my workspace.
>
>
>
> Help please?
>
>
>
> Best regards
>
>
>
> // Johan L
>
>
>
> ****************************************************************************
> ***************
>
> Johan Lindberg
>
> Royal Institute of Technology
>
> AlbaNova University Center
>
> Stockholm Center for Physics, Astronomy and Biotechnology
>
> Department of Molecular Biotechnology
>
> Visiting address:
>
> Roslagstullsbacken 21, Floor 3
>
> 106 91 Stockholm, Sweden
>
> Delivering address:
>
> Roslagstullsbacken 30B
>
> 104 06 Stockholm, Sweden
>
> Phone (office) +46 8 553 783 44
>
> Fax + 46 8 553 784 81
>
> http://www.ktharray.se/
>
> ****************************************************************************
> ***************
>
>
>
>
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>
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