[BioC] Functions

[James W. MacDonald]

Hi Ipsitha,

On 6/7/2013 12:26 PM, Ipsitha [guest] wrote:
> Hi
>
> I am trying to do some data analysis using R and Bioconductor.  I have a function to read my data called "ReadAffyData" and a function to plot the data called "preqc".  I want to know if there is any way I can extract information (read: Data) from the ReadAffyData function into preqc in order to produce plots? I have not completely understood the inheritance in R and I am getting errors similar to the one below. I am new to R and could do with any help in this aspect!
>
> Code:
> ReadAffyData<- function( filename ) {
>
>          require(affy)
>          require(annotate)
>
>          Cov<- read.table( filename, sep="\t", header=1, quote="", comment="" )
>      if( ! all( c( "Filename", "Label", "Repl", "Trt" ) %in% colnames( Cov ) ) )
>          {
>          stop( "Missing mandatory column" )
>      }
>
>          Cov<- Cov[order(Cov$Trt),]
>          i<- table(Cov$Trt)
>          Cov$Repl<- unlist( lapply( i, function( j ) 1:j ) )
>          Cov$Label<- paste( as.character( Cov$Trt ), Cov$Repl, sep=":" )
>          rownames(Cov)<- as.character(Cov$Label)
>
>          tmp1<- colnames( Cov )
>      tmp2<- rep( "", length( Cov ) )
>
>          for( i in 1:length( tmp2 ) )
>          {
>          tmp2[i]<- paste( sort( unique( as.character( Cov[,i] ) ) ), collapse="/" )
>      }
>
>          labelDescription<- data.frame( labelDescription=tmp2 )
>
>      rownames( labelDescription )<- tmp1
>      tmp<- new( "AnnotatedDataFrame", data=Cov, varMetadata=labelDescription)
>
>          Data<- ReadAffy( sampleNames=as.character( Cov$Label ),phenoData=tmp, verbose=TRUE )
> }

This function doesn't return anything. You can end the function in one 
of three ways. The last lines can be

ReadAffy(sampleNames=as.character( Cov$Label ),phenoData=tmp, verbose=TRUE )
}

or

Data <- ReadAffy( sampleNames=as.character( Cov$Label ),phenoData=tmp, 
verbose=TRUE )
Data
}

or

Data <- ReadAffy( sampleNames=as.character( Cov$Label ),phenoData=tmp, 
verbose=TRUE )
return(Data)
}

But your function as written creates the Data object and then closes 
without returning that object to you.

>
> preQC<- function(name){
> ReadAffyData(name)
> plotDensity( log2( pm( Data ) ), xlab="Log2( Intensity )", ylab="Density", main="Raw(PM)")
> }

And even if you fix your ReadAffyData function to return the Data 
object, this function won't work, because you aren't capturing the 
output in an object. You need to do this:

preQC<- function(name){
Data<- ReadAffyData(name)
plotDensity( log2( pm( Data ) ), xlab="Log2( Intensity )", ylab="Density", main="Raw(PM)")
}

Best,

Jim



>
> preQC("cov.txt")
> 1 reading C:/CEL/GSM311471.CEL ...instantiating an AffyBatch (intensity a 506944x24 matrix)...done.
> Reading in : C:/CEL/GSM311471.CEL
> Reading in : C:/CEL/GSM311472.CEL
> Reading in : C:/CEL/GSM311473.CEL
> Reading in : C:/CEL/GSM311474.CEL
> Reading in : C:/CEL/GSM311475.CEL
> .
> .
> .
> Error in pm(Data) :
>    error in evaluating the argument 'object' in selecting a method for function 'pm': Error: object 'Data' not found
>
>
>   -- output of sessionInfo():
>
> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252    LC_MONETARY=English_India.1252
> [4] LC_NUMERIC=C                   LC_TIME=English_India.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] annotate_1.38.0      AnnotationDbi_1.22.6 affy_1.38.1          Biobase_2.20.0       BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.28.0         BiocInstaller_1.10.1  DBI_0.2-7             IRanges_1.18.1        preprocessCore_1.22.0
>   [6] RSQLite_0.11.4        stats4_3.0.1          tools_3.0.1           XML_3.96-1.1          xtable_1.7-1
> [11] zlibbioc_1.6.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099