seqnames on dbSNP object error
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Mark Cowley ▴ 910
@mark-cowley-2951
Last seen 9.6 years ago
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. # 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]]
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@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States
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
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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
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