[BioC] PICS: vignette code outdated (use of GenomeData-object)

[Valerie Obenchain]

Hi Sam,

The error is being thrown from the .useRanges function in the 
setMethods.R file of the PICS package. When RangedData is coerced to 
GenomeData there is a call to .useRanges which has the deprecated message,


.useRanges <- function() {
   .Deprecated(msg = "Storing reads only by their start positions is 
deprecated. Please use a range representation like GRanges.")
}


I have cc'd the package maintainers so they can fix the problem.


Valerie



On 05/05/2011 04:49 AM, Samuel Wuest wrote:
> Hello,
>
> I am trying to follow the example outlined in the PICS vignette in
> order to analyse a ChIP-Seq dataset, but the code does not actually
> work anymore (see code below).
>
> The GenomeData-object used for the analysis (i.e. the
> segmentReads-command) cannot be constructed anymore, it seems that the
> respective conversion from a RangedData-object to a GenomeData-object
> is deprecated.
>
> I am not sure why the conversion from a RangedData to a
> GenomeData-object should work, actually, as the RangedData-contains
> information on start and end of the reads.
> I can convert the RangedData into a GRanges object, but the PICS
> command segmentReads()-wouldn't work with that.
> Any suggestions?
>
> Thanks for any help, best, Sam
>
> ### Following the R-script according to the PICS vignette:
>
>> path<-system.file("extdata",package="PICS")
>> #Read the experiment :
>> dataIP<-read.table(file.path(path,"Treatment_tags_chr21_sort.bed"),header=TRUE,colClasses=c("factor","integer","integer","factor"))
>> dataIP<-as(dataIP,"RangedData")
>> dataIP<-as(dataIP,"GenomeData")
> Warning message:
> Storing reads only by their start positions is deprecated. Please use
> a range representation like GRanges.
>> dataCont<-read.table(file.path(path,"Input_tags_chr21_sort.bed"),header=TRUE,colClasses=c("factor","integer","integer","factor"))
>> dataCont<-as(dataCont,"RangedData")
>> dataCont<-as(dataCont,"GenomeData")
> Warning message:
> Storing reads only by their start positions is deprecated. Please use
> a range representation like GRanges.
> ### looking at the object created here shows that it is basically empty:
>> dataCont
> A GenomeData instance
> chromosomes(1): chr21
> ### the "segmentReads"-command works but is not very useful, for the
> dataIP and dataCont-objects are both empty:
>> seg<-segmentReads(dataIP, dataC=dataCont, minReads=1)
> ### alternatively, trying to provide a GRanges-objects to the
> segmentReads-command:
>> dataIP<-read.table(file.path(path,"Treatment_tags_chr21_sort.bed"),header=TRUE,colClasses=c("factor","integer","integer","factor"))
>> dataIP<-as(dataIP,"RangedData")
>> dataIP<- as(dataIP, "GRanges")
>> seg<-segmentReads(dataIP, dataC=dataCont, minReads=1)
> Error in segmentReads(dataIP, dataC = dataCont, minReads = 1) :
>    The input data should be 'GenomeData' objects
>
> ### I am not sure whether the problem could be fixed using a different
> constructor for GenomeData-objects?
>
> Here is my sessionInfo():
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] PICS_1.4.0          BSgenome_1.18.2     Biostrings_2.18.2
> GenomicRanges_1.2.1 IRanges_1.8.5
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.10.0
>
>
> -------------------------------------------------------
> Samuel Wuest
> Smurfit Institute of Genetics
> Trinity College Dublin
> Dublin 2, Ireland
> Phone: +353-1-896 2444
> Web: http://www.tcd.ie/Genetics/wellmer-2/index.html
> Email: wuests at tcd.ie
>
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