rtracklayer error?
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 9.6 years ago
Hi, I was just trying out the rtracklayer package with the example given in the bioinformatics paper on rtracklayer. Here is my code and the error statement: > library(IRanges) > library(rtracklayer) > data(targets) > tt <- >with(targets,GenomicData(IRanges(start,end),target,strand=strand,chro m=chrom)) > class(tt) [1] "RangedData" attr(,"package") [1] "IRanges" > session <- browserSession() > session$targets <- tt Error in FUN(X[[1L]], ...) : Invalid chromosomes for hg19: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT My sessionInfo and traceback for the error are: > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] hash_2.1.0 biomaRt_2.8.0 rtracklayer_1.12.2 RCurl_1.5-0 bitops_1.0-4.1 [6] IRanges_1.10.4 pvclust_1.2-2 les_1.2.0 fdrtool_1.2.7 ggplot2_0.8.9 [11] proto_0.3-9.2 reshape_0.8.4 plyr_1.5.2 loaded via a namespace (and not attached): [1] Biostrings_2.20.1 boot_1.2-43 BSgenome_1.20.0 gdata_2.8.1 GenomicRanges_1.4.6 [6] gplots_2.8.0 gtools_2.6.2 RColorBrewer_1.0-2 tools_2.13.0 XML_3.4-0 > traceback() 15: stop("Invalid chromosomes for ", genome(session), ": ", paste(badSpaces, collapse = ", ")) 14: FUN(X[[1L]], ...) 13: lapply(split(X, group), FUN, ...) 12: tapply(value, unlist(genomes), function(tracks) { genome <- genome(tracks[[1]]) if (length(genome)) genome(session) <- genome spaces <- unlist(lapply(tracks, names)) badSpaces <- setdiff(spaces, seqnames(session)) if (length(badSpaces)) stop("Invalid chromosomes for ", genome(session), ": ", paste(badSpaces, collapse = ", ")) }) 11: normArgTrackData(value, session) 10: .local(object, ..., value = value) 9: `track<-`(`*tmp*`, name, ..., value = <s4 object="" of="" class="" "rangeddatalist"="">) 8: `track<-`(`*tmp*`, name, ..., value = <s4 object="" of="" class="" "rangeddatalist"="">) 7: .local(object, ..., value = value) 6: `track<-`(`*tmp*`, i, ..., value = <s4 object="" of="" class="" "rangeddata"="">) 5: `track<-`(`*tmp*`, i, ..., value = <s4 object="" of="" class="" "rangeddata"="">) 4: `[[<-`(`*tmp*`, name, value = <s4 object="" of="" class="" "rangeddata"="">) 3: `[[<-`(`*tmp*`, name, value = <s4 object="" of="" class="" "rangeddata"="">) 2: `$<-`(`*tmp*`, "targets", value = <s4 object="" of="" class="" "rangeddata"="">) 1: `$<-`(`*tmp*`, "targets", value = <s4 object="" of="" class="" "rangeddata"="">) [[alternative HTML version deleted]]
rtracklayer rtracklayer • 1.1k views
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@michael-lawrence-3846
Last seen 2.3 years ago
United States
You just need to paste("chr", targets$chrom). I will update the targets.rda so that is already done. Things have changed a bit since that paper was written. Michael On Tue, Jun 7, 2011 at 10:16 AM, Tim Smith <tim_smith_666@yahoo.com> wrote: > Hi, > > I was just trying out the rtracklayer package with the example given in the > bioinformatics paper on rtracklayer. Here is my code and the error > statement: > > > library(IRanges) > > library(rtracklayer) > > data(targets) > > tt <- > > >with(targets,GenomicData(IRanges(start,end),target,strand=strand,ch rom=chrom)) > > class(tt) > [1] "RangedData" > attr(,"package") > [1] "IRanges" > > > session <- browserSession() > > session$targets <- tt > Error in FUN(X[[1L]], ...) : > Invalid chromosomes for hg19: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, > 14, > 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT > > > My sessionInfo and traceback for the error are: > > > > sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > > other attached packages: > [1] hash_2.1.0 biomaRt_2.8.0 rtracklayer_1.12.2 RCurl_1.5-0 > bitops_1.0-4.1 > > [6] IRanges_1.10.4 pvclust_1.2-2 les_1.2.0 fdrtool_1.2.7 > ggplot2_0.8.9 > > [11] proto_0.3-9.2 reshape_0.8.4 plyr_1.5.2 > > loaded via a namespace (and not attached): > [1] Biostrings_2.20.1 boot_1.2-43 BSgenome_1.20.0 > gdata_2.8.1 GenomicRanges_1.4.6 > [6] gplots_2.8.0 gtools_2.6.2 RColorBrewer_1.0-2 > tools_2.13.0 XML_3.4-0 > > > > > > traceback() > 15: stop("Invalid chromosomes for ", genome(session), ": ", > paste(badSpaces, > collapse = ", ")) > 14: FUN(X[[1L]], ...) > 13: lapply(split(X, group), FUN, ...) > 12: tapply(value, unlist(genomes), function(tracks) { > genome <- genome(tracks[[1]]) > if (length(genome)) > genome(session) <- genome > spaces <- unlist(lapply(tracks, names)) > badSpaces <- setdiff(spaces, seqnames(session)) > if (length(badSpaces)) > stop("Invalid chromosomes for ", genome(session), ": ", > paste(badSpaces, collapse = ", ")) > }) > 11: normArgTrackData(value, session) > 10: .local(object, ..., value = value) > 9: `track<-`(`*tmp*`, name, ..., value = <s4 object="" of="" class=""> "RangedDataList">) > 8: `track<-`(`*tmp*`, name, ..., value = <s4 object="" of="" class=""> "RangedDataList">) > 7: .local(object, ..., value = value) > 6: `track<-`(`*tmp*`, i, ..., value = <s4 object="" of="" class="" "rangeddata"="">) > 5: `track<-`(`*tmp*`, i, ..., value = <s4 object="" of="" class="" "rangeddata"="">) > 4: `[[<-`(`*tmp*`, name, value = <s4 object="" of="" class="" "rangeddata"="">) > 3: `[[<-`(`*tmp*`, name, value = <s4 object="" of="" class="" "rangeddata"="">) > 2: `$<-`(`*tmp*`, "targets", value = <s4 object="" of="" class="" "rangeddata"="">) > 1: `$<-`(`*tmp*`, "targets", value = <s4 object="" of="" class="" "rangeddata"="">) > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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