Dear list, I have been trying to use seqmentSeq package. Running the examples in the package was successful, but on my data gives error at "readGeneric" function: here is my test code and attached data files (was attached, but held for review because it is bigger than 40 KB). libfiles <- c("V010.mapped_tt.txt","V010.mapped_tt2.txt") libnames <- c( "tt1","tt2") replicates <- c("fGS_OSS","fGS_OSS") aD <- readGeneric(files = libfiles, dir = paste(datadir,"test/",sep=""), header = TRUE, replicates = replicates, libnames = libnames, chrs = c("chr2L","chr2R"), chrlens = c(23011544,21146708), gap = 100,polyLength = 10) Reading files......done! Analysing tags..........done! Error in validObject(.Object) : invalid class “GRanges” object: 'ranges' contains values outside of sequence bounds debugging message: Enter a frame number, or 0 to exit 1: readGeneric(files = libfiles, dir = paste(datadir, "test/", sep = ""), head 2: .processTags(Tags, verbose = verbose, estimationType = estimationType, gap 3: `seqinfo<-`(`*tmp*`, new2old = chrmatch, value = <s4 object="" of="" class="" "seqin="" 4:="" `seqinfo<-`(`*tmp*`,="" new2old="chrmatch," value="&lt;S4" object="" of="" class="" "seqin="" 5:="" update(x,="" seqnames="makeNewSeqnames(x," new2old,="" seqlevels(value)),="" seqinfo="" 6:="" update(x,="" seqnames="makeNewSeqnames(x," new2old,="" seqlevels(value)),="" seqinfo="" 7:="" initialize(object,="" ...)="" 8:="" initialize(object,="" ...)="" 9:="" validobject(.object)=""> sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Rmpi_0.5-9 snow_0.3-7 segmentSeq_1.6.0 [4] ShortRead_1.12.0 latticeExtra_0.6-19 RColorBrewer_1.0-5 [7] Rsamtools_1.6.1 lattice_0.20-0 GenomicRanges_1.6.3 [10] baySeq_1.8.0 ggplot2_0.8.9 proto_0.3-9.2 [13] reshape_0.8.4 plyr_1.6 limma_3.10.0 [16] Biostrings_2.22.0 IRanges_1.12.1 loaded via a namespace (and not attached): [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 hwriter_1.3 [5] RCurl_1.7-0 rtracklayer_1.14.3 tools_2.14.0 XML_3.4-3 [9] zlibbioc_1.0.0 Thank you very much for the help, Jean [[alternative HTML version deleted]]

Hi -- On 11/19/2011 07:55 AM, jiayu wen wrote: > Dear list, > > I have been trying to use seqmentSeq package. Running the examples in the package was successful, but on my data gives error at "readGeneric" function: > > here is my test code and attached data files (was attached, but held for review because it is bigger than 40 KB). > libfiles<- c("V010.mapped_tt.txt","V010.mapped_tt2.txt") > libnames<- c( "tt1","tt2") > replicates<- c("fGS_OSS","fGS_OSS") > aD<- readGeneric(files = libfiles, dir = paste(datadir,"test/",sep=""), header = TRUE, > replicates = replicates, libnames = libnames, > chrs = c("chr2L","chr2R"), chrlens = c(23011544,21146708), gap = 100,polyLength = 10) > > > Reading files......done! > Analysing tags..........done! > Error in validObject(.Object) : > invalid class ?GRanges? object: 'ranges' contains values outside of sequence bounds I don't have experience with segmentSeq but this error occurs when a GRanges object is constructed with ranges that are outside the bounds of the sequence lengths (10 > 9 below) > GRanges("A", IRanges(1, 10), seqlengths=c(A=9)) Error in validObject(.Object) : invalid class "GRanges" object: 'ranges' contains values outside of sequence bounds I'd guess that your reads dangled over the edges of the chromosomes a little, and that a work-around is to expand chrlens by a few nucleotides. Alternatively, this could be a real error, e.g., because the lengths you provide do not match the lengths of the chromosomes in the alignment. Hope that helps, Martin > > debugging message: > > Enter a frame number, or 0 to exit > > 1: readGeneric(files = libfiles, dir = paste(datadir, "test/", sep = ""), head > 2: .processTags(Tags, verbose = verbose, estimationType = estimationType, gap > 3: `seqinfo<-`(`*tmp*`, new2old = chrmatch, value =<s4 object="" of="" class="" "seqin=""> 4: `seqinfo<-`(`*tmp*`, new2old = chrmatch, value =<s4 object="" of="" class="" "seqin=""> 5: update(x, seqnames = makeNewSeqnames(x, new2old, seqlevels(value)), seqinfo > 6: update(x, seqnames = makeNewSeqnames(x, new2old, seqlevels(value)), seqinfo > 7: initialize(object, ...) > 8: initialize(object, ...) > 9: validObject(.Object) > > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] Rmpi_0.5-9 snow_0.3-7 segmentSeq_1.6.0 > [4] ShortRead_1.12.0 latticeExtra_0.6-19 RColorBrewer_1.0-5 > [7] Rsamtools_1.6.1 lattice_0.20-0 GenomicRanges_1.6.3 > [10] baySeq_1.8.0 ggplot2_0.8.9 proto_0.3-9.2 > [13] reshape_0.8.4 plyr_1.6 limma_3.10.0 > [16] Biostrings_2.22.0 IRanges_1.12.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.14.0 bitops_1.0-4.1 BSgenome_1.22.0 hwriter_1.3 > [5] RCurl_1.7-0 rtracklayer_1.14.3 tools_2.14.0 XML_3.4-3 > [9] zlibbioc_1.0.0 > > > Thank you very much for the help, > > Jean > [[alternative HTML version deleted]] > > > > > _______________________________________________ > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793