[BioC] AnnBuilder question: about how to retrieve information when using a built package?

[Ting-Yuan Liu]

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/
> 
> ****************************************************************************
> *************** 
> 
>  
> 
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>