Question: New SNPlocs data package for Human (dbSNP BUILD 131)
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gravatar for Hervé Pagès
9.5 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:
Hi Lin, The new package is ready and available thru biocLite(): > library(BSgenome) > available.SNPs() BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). [1] "SNPlocs.Hsapiens.dbSNP.20071016" "SNPlocs.Hsapiens.dbSNP.20080617" [3] "SNPlocs.Hsapiens.dbSNP.20090506" "SNPlocs.Hsapiens.dbSNP.20100427" Only the source package is available for now. Binaries for Windows and Mac will follow soon, but you can still install the source package on these OS by using the 'type="source"' option in biocLite(). dbSNP is growing fast and this new package (BUILD 131) is about 50% bigger than the previous one (BUILD 130): SNPlocs.Hsapiens.dbSNP.20090506 | SNPlocs.Hsapiens.dbSNP.20100427 BUILD 130 | BUILD 131 Ref. genome: NCBI Build 36.1 | Ref. genome: GRCh37 Compatible with: UCSC hg18 | Compatible with: UCSC hg19 | (except for chrM) size: 81MB | size: 123MB nb of SNPs: 11846489 | nb of SNPs: 17434679 See the full description here http://bioconductor.org/packages/2.6/data/annotation/html/SNPlocs.Hsap iens.dbSNP.20100427.html for why SNPs on the mitochondrion chromosome are not compatible with hg19 chrM. I tried to improve the man page of this new package over the previous SNPlocs pkgs. In particular now it briefly explains how SNPs from dbSNP were filtered (impossible to keep everything, dbSNP contains much more stuff than just SNPs), and the examples section has more examples. Also a new feature is that you can now extract SNPs from 1 or more chromosomes at the same time and get the result in a GRanges object. Just use as.GRanges=TRUE when calling getSNPlocs(). Please make sure you update BSgenome to >= 1.16.1 (available in about 12 hours thru biocLite) before you try to inject those SNPs in BSgenome.Hsapiens.UCSC.hg19. Let me know if you have any questions. Feedback from SNPlocs users will be greatly appreciated. Cheers, H. Lin Tang wrote: > Hi, Dear Herv? > > The new dbSNP build is available and the human genome sequence is now hg19. Would you please updated the R package for the SNP locations? > > Thank you very much! > > Regards, > Lin > > Lin Tang, Ph.D. > Scientist II, Informatics | Sequenom Inc. > T: 1 858 202 9106 | F: 1 858 202 9084 > > > > > THIS EMAIL MESSAGE IS FOR THE SOLE USE OF THE INTENDED RECIPIENT(S) AND MAY CONTAIN CONFIDENTIAL INFORMATION. ANY UNAUTHORIZED REVIEW, USE, DISCLOSURE OR DISTRIBUTION IS PROHIBITED. IF YOU ARE NOT THE INTENDED RECIPIENT, PLEASE CONTACT THE SENDER BY REPLY EMAIL AND DESTROY ALL COPIES OF THE ORIGINAL MESSAGE. -- 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
cancer bsgenome snplocs • 632 views
ADD COMMENTlink modified 9.5 years ago • written 9.5 years ago by Hervé Pagès ♦♦ 14k
Answer: New SNPlocs data package for Human (dbSNP BUILD 131)
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gravatar for Hervé Pagès
9.5 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:
Hi Lin, Lin Tang wrote: > Hi, Dear Herv? > > Thanks so much for quickly assemble the new package. I have installed the hg19 and the new SNP packages, but I get error when try to "injectNSPs", do you have any clue what the problem might be? Thanks! > > Regards, > Lin > >> library("BSgenome.Hsapiens.UCSC.hg19") >> library("SNPlocs.Hsapiens.dbSNP.20100427") >> HsWithSNPs = injectSNPs(Hsapiens, "SNPlocs.Hsapiens.dbSNP.20100427") > Error in injectSNPs(Hsapiens, "SNPlocs.Hsapiens.dbSNP.20100427") : > sequence names in package SNPlocs.Hsapiens.dbSNP.20100427 are not compatible with those in genome 'x' The injection mechanism has changed. Now it uses an internal (defined in the SNPlocs package) to translate from UCSC chromosome names to NCBI/dbSNP chromosome names. This new mechanism is implemented in BSgenome 1.16.1. This is why, in my previous email, I wrote: Please make sure you update BSgenome to >= 1.16.1 (available in about 12 hours thru biocLite) before you try to inject those SNPs in BSgenome.Hsapiens.UCSC.hg19. Cheers, H. >> Hsapiens > Human genome > | > | organism: Homo sapiens (Human) > | provider: UCSC > | provider version: hg19 > | release date: Feb. 2009 > | release name: Genome Reference Consortium GRCh37 > | > | single sequences (see '?seqnames'): > | chr1 chr2 chr3 chr4 > | chr5 chr6 chr7 chr8 > | chr9 chr10 chr11 chr12 > | chr13 chr14 chr15 chr16 > | chr17 chr18 chr19 chr20 > | chr21 chr22 chrX chrY > | chrM chr1_gl000191_random chr1_gl000192_random chr4_ctg9_hap1 > | chr4_gl000193_random chr4_gl000194_random chr6_apd_hap1 chr6_cox_hap2 > | chr6_dbb_hap3 chr6_mann_hap4 chr6_mcf_hap5 chr6_qbl_hap6 > | chr6_ssto_hap7 chr7_gl000195_random chr8_gl000196_random chr8_gl000197_random > | chr9_gl000198_random chr9_gl000199_random chr9_gl000200_random chr9_gl000201_random > | chr11_gl000202_random chr17_ctg5_hap1 chr17_gl000203_random chr17_gl000204_random > | chr17_gl000205_random chr17_gl000206_random chr18_gl000207_random chr19_gl000208_random > | chr19_gl000209_random chr21_gl000210_random chrUn_gl000211 chrUn_gl000212 > | chrUn_gl000213 chrUn_gl000214 chrUn_gl000215 chrUn_gl000216 > | chrUn_gl000217 chrUn_gl000218 chrUn_gl000219 chrUn_gl000220 > | chrUn_gl000221 chrUn_gl000222 chrUn_gl000223 chrUn_gl000224 > | chrUn_gl000225 chrUn_gl000226 chrUn_gl000227 chrUn_gl000228 > | chrUn_gl000229 chrUn_gl000230 chrUn_gl000231 chrUn_gl000232 > | chrUn_gl000233 chrUn_gl000234 chrUn_gl000235 chrUn_gl000236 > | chrUn_gl000237 chrUn_gl000238 chrUn_gl000239 chrUn_gl000240 > | chrUn_gl000241 chrUn_gl000242 chrUn_gl000243 chrUn_gl000244 > | chrUn_gl000245 chrUn_gl000246 chrUn_gl000247 chrUn_gl000248 > | chrUn_gl000249 > | > | multiple sequences (see '?mseqnames'): > | upstream1000 upstream2000 upstream5000 > | > | (use the '$' or '[[' operator to access a given sequence) > > > > THIS EMAIL MESSAGE IS FOR THE SOLE USE OF THE INTENDED RECIPIENT(S) AND MAY CONTAIN CONFIDENTIAL INFORMATION. ANY UNAUTHORIZED REVIEW, USE, DISCLOSURE OR DISTRIBUTION IS PROHIBITED. IF YOU ARE NOT THE INTENDED RECIPIENT, PLEASE CONTACT THE SENDER BY REPLY EMAIL AND DESTROY ALL COPIES OF THE ORIGINAL MESSAGE. -- 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
ADD COMMENTlink written 9.5 years ago by Hervé Pagès ♦♦ 14k
Hervé Pagès wrote: [...] > The injection mechanism has changed. Now it uses an internal (defined ^^^^^^^^^^^ I meant: an internal table H. > in the SNPlocs package) to translate from UCSC chromosome names to > NCBI/dbSNP chromosome names. This new mechanism is implemented in > BSgenome 1.16.1. This is why, in my previous email, I wrote: > > Please make sure you update BSgenome to >= 1.16.1 (available in > about 12 hours thru biocLite) before you try to inject those SNPs > in BSgenome.Hsapiens.UCSC.hg19. > > Cheers, > H.
ADD REPLYlink written 9.5 years ago by Hervé Pagès ♦♦ 14k
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