cheers Herv?, that works well M On 10/04/2011, at 5:38 AM, Hervé Pagès wrote: > Hi Mark, > > Sorry for the late answer. > > On 11-04-05 08:38 PM, Mark Cowley wrote: >> Hi folks, >> i'm trying to compare a few different GRanges objects (such as mutations made by me, SNPs from SNPlocs.Hsapiens.dbSNP.20101109 and transcripts from GenomicFeatures), and since the dbSNP data package uses 'ch1' as opposed to 'chr1', I need to coerce the seqnames so that they can be matched. >> Here's the error: >> >>> snps<- getSNPlocs("ch17", as.GRanges=TRUE) >>> seqnames(snps)<- rep('chr17', length(snps)) >> Error in validObject(.Object) : >> invalid class "Seqinfo" object: 'seqnames(x)' must be an unnamed character vector with no NAs >> >> According to the man page this should be doable: >> ?`seqnames,GRanges-method` >> ?seqnames(x)?, ?seqnames(x)<- value?: Gets or sets the sequence names. >> ?value? can be an Rle object, character vector, or factor. > > There is an example at the bottom of the man page showing how to > do this. In your case: > > seqnames(snps) <- sub("ch", "chr", seqnames(snps)) > > Note that the mechanism for renaming, dropping, adding or reordering > the names of the underlying sequences has been revisited in BioC 2.8 > (soon-to-be-released). The user will do this thru the seqlevels getter > and setter. > > Cheers, > H. > >> >> # Try using an Rle: >>> seqnames(snps)<- Rle(rep('chr17', length(snps))) >> Error in validObject(.Object) : >> invalid class "Seqinfo" object: 'seqnames(x)' must be an unnamed character vector with no NAs >> >> >> Reproducible code in a fresh R session: >> library(SNPlocs.Hsapiens.dbSNP.20101109) >> snps<- getSNPlocs("ch17", as.GRanges=TRUE) >> seqnames(snps)<- rep('chr17', length(snps)) >> Error in validObject(.Object) : >> invalid class "Seqinfo" object: 'seqnames(x)' must be an unnamed character vector with no NAs >> >> snps >> GRanges with 641905 ranges and 2 elementMetadata values >> seqnames ranges strand | RefSNP_id alleles_as_ambig >> <rle> <iranges> <rle> |<character> <character> >> [1] ch17 [ 293, 293] * | 9747578 R >> [2] ch17 [ 828, 828] * | 62053745 Y >> [3] ch17 [ 834, 834] * | 9747082 R >> [4] ch17 [1389, 1389] * | 62053747 R >> [5] ch17 [1397, 1397] * | 34845611 Y >> [6] ch17 [1665, 1665] * | 34151105 Y >> [7] ch17 [1869, 1869] * | 62053748 W >> [8] ch17 [1880, 1880] * | 77383171 Y >> [9] ch17 [1897, 1897] * | 75157665 R >> ... ... ... ... ... ... ... >> [641897] ch17 [81180274, 81180274] * | 74430365 R >> [641898] ch17 [81189713, 81189713] * | 74334266 Y >> [641899] ch17 [81189731, 81189731] * | 75151244 W >> [641900] ch17 [81190324, 81190324] * | 76196913 S >> [641901] ch17 [81190344, 81190344] * | 78502756 R >> [641902] ch17 [81190367, 81190367] * | 2850176 Y >> [641903] ch17 [81190378, 81190378] * | 71264801 R >> [641904] ch17 [81190400, 81190400] * | 74838487 R >> [641905] ch17 [81193098, 81193098] * | 77334326 R >> >> seqlengths >> ch1 ch2 ch3 ch4 ch5 ch6 ch7 ch8 ... ch19 ch20 ch21 ch22 chX chY chMT >> NA NA NA NA NA NA NA NA ... NA NA NA NA NA NA NA >> >>> sessionInfo() >> R version 2.12.1 (2010-12-16) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] SNPlocs.Hsapiens.dbSNP.20101109_0.99.2 >> [2] GenomicRanges_1.2.3 >> [3] IRanges_1.8.8 >> >> loaded via a namespace (and not attached): >> [1] tools_2.12.1 >> >> >> >> >> [[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 > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319