PICS: vignette code outdated (use of GenomeData-object)
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Samuel Wuest ▴ 330
@samuel-wuest-2821
Last seen 8.3 years ago
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"),h eader=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"),hea der=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"),h eader=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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@valerie-obenchain-4275
Last seen 11 months ago
United States
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"),he ader=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
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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 >
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