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"),h eader=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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >