[BioC] PICS: vignette code outdated (use of GenomeData-object)

[Raphael Gottardo]

We are working on this. 

Sent from my iPad

On May 13, 2011, at 12:00 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:

> 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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>