Hi Simon, The windows binary of SNPlocs.Hsapiens.dbSNP.20101109 is now available. Valerie On 01/07/11 10:48, Valerie Obenchain wrote: > Hi Simon, > > Please see responses below. > > > > On 01/06/2011 09:47 AM, Simon No?l wrote: > >> Thank you. Sorry for the delay. As I say, on my >> computer, thing run really slowy... I have no error but I have some >> warning and no result... >> >> >> >> library("IRanges") >> library("GenomicRanges") >> library("GenomicFeatures") >> #? changer si une version plus r?cente de la librairie est t?l?charg?e. >> library(SNPlocs.Hsapiens.dbSNP.20101109) >> >> >>> getSNPcount() >>> >> ch1 ch2 ch3 ch4 ch5 ch6 ch7 ch8 ch9 ch10 >> >> 1849438 1936836 1613418 1613633 1453710 1446827 1335745 1243129 >> 995075 1158707 >> ch11 ch12 ch13 ch14 ch15 ch16 ch17 ch18 ch19 ch20 >> >> 1147722 1105364 815729 740129 657719 757926 641905 645646 >> 520666 586708 >> ch21 ch22 chX chY chMT >> 338254 331060 529608 67438 624 >> >>> ch22snps<- getSNPlocs("ch22") >>> ch22snps[1:5, ] >>> >> RefSNP_id alleles_as_ambig loc >> 1 56342815 K 16050353 >> 2 7288968 S 16050994 >> 3 6518357 M 16051107 >> 4 7292503 R 16051209 >> 5 6518368 Y 16051241 >> >>> >>> makeGRangesFromRefSNPids<- function(myids) >>> >> + { >> + ans_seqnames<- character(length(myids)) >> + ans_seqnames[]<- "unknown" >> + ans_locs<- integer(length(myids)) >> + for (seqname in names(getSNPcount())) { >> + locs<- getSNPlocs(seqname) >> + ids<- paste("rs", locs$RefSNP_id, sep="") >> + myrows<- match(myids, ids) >> + ans_seqnames[!is.na(myrows)]<- seqname >> + ans_locs[!is.na(myrows)]<- locs$loc[myrows] >> + } >> + GRanges(seqnames=ans_seqnames, >> + IRanges(start=ans_locs, width=1), >> + RefSNP_id=myids) >> + } >> >>> >>> myids<- c("rs7547453", "rs2840542", "rs1999527", "rs4648545", >>> >> "rs10915459", "rs16838750", "rs12128230", "rs999999999") >> >>> mysnps<- makeGRangesFromRefSNPids(myids) >>> >> Warning message: >> In ans_locs[!is.na(myrows)]<- locs$loc[myrows] : >> number of items to replace is not a multiple of replacement length >> >>> mysnps # a GRanges object with 1 SNP per row >>> >> GRangeswith 8 ranges and 1 elementMetadata value >> seqnames ranges strand | RefSNP_id >> <rle> <iranges> <rle> |<character> >> [1] ch1 [2195117, 2195117] * | rs7547453 >> [2] ch1 [2291680, 2291680] * | rs2840542 >> [3] ch1 [3256108, 3256108] * | rs1999527 >> [4] ch1 [3577321, 3577321] * | rs4648545 >> [5] ch1 [4230463, 4230463] * | rs10915459 >> [6] ch1 [4404344, 4404344] * | rs16838750 >> [7] ch1 [4501911, 4501911] * | rs12128230 >> [8] unknown [ 0, 0] * | rs999999999 >> seqlengths >> ch1 unknown >> NA NA >> >>> txdb<- makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene") >>> >> Downloadthe refGene table ... OK >> Downloadthe refLink table ... OK >> Extractthe 'transcripts' data frame ... OK >> Extractthe 'splicings' data frame ... OK >> Downloadand preprocess the 'chrominfo' data frame ... OK >> Preparethe 'metadata' data frame ... OK >> Makethe TranscriptDb object ... OK >> Il y a eu 50 avis ou plus (utilisez warnings() pour voir les 50 premiers) >> >>> txdb >>> >> TranscriptDbobject: >> | Db type: TranscriptDb >> | Data source: UCSC >> | Genome: hg19 >> | UCSC Table: refGene >> | Type of Gene ID: Entrez Gene ID >> | Full dataset: yes >> | transcript_nrow: 38098 >> | exon_nrow: 230201 >> | cds_nrow: 204683 >> | Db created by: GenomicFeatures package from Bioconductor >> | Creation time: 2011-01-06 11:55:44 -0500 (Thu, 06 Jan 2011) >> | GenomicFeatures version at creation time: 1.2.3 >> | RSQLite version at creation time: 0.9-4 >> | DBSCHEMAVERSION: 1.0 >> >>> #voir pour exonsBy() ? la place de tx >>> txExon = exonsBy(txdb, by= "tx") >>> txExon >>> >> GRangesListof length 38098 >> $1 >> GRanges with 25 ranges and 3 elementMetadata values >> seqnames ranges strand >> | exon_id exon_name exon_rank >> <rle> <iranges> <rle> |<integer> <character> >> <integer> >> [1] chr1 [66999825, 67000051] + | 1 >> NA 1 >> [2] chr1 [67091530, 67091593] + | 2 >> NA 2 >> [3] chr1 [67098753, 67098777] + | 3 >> NA 3 >> [4] chr1 [67101627, 67101698] + | 4 >> NA 4 >> [5] chr1 [67105460, 67105516] + | 5 >> NA 5 >> [6] chr1 [67108493, 67108547] + | 6 >> NA 6 >> [7] chr1 [67109227, 67109402] + | 7 >> NA 7 >> [8] chr1 [67126196, 67126207] + | 8 >> NA 8 >> [9] chr1 [67133213, 67133224] + | 9 >> NA 9 >> ... ... ... ... ... ... >> ... ... >> [17] chr1 [67155873, 67155999] + | 17 >> NA 17 >> [18] chr1 [67161117, 67161176] + | 18 >> NA 18 >> [19] chr1 [67184977, 67185088] + | 19 >> NA 19 >> [20] chr1 [67194947, 67195102] + | 20 >> NA 20 >> [21] chr1 [67199431, 67199563] + | 21 >> NA 21 >> [22] chr1 [67205018, 67205220] + | 22 >> NA 22 >> [23] chr1 [67206341, 67206405] + | 23 >> NA 23 >> [24] chr1 [67206955, 67207119] + | 24 >> NA 24 >> [25] chr1 [67208756, 67210768] + | 25 >> NA 25 >> ... >> <38097 more elements> >> >> seqlengths >> chr1 chr2 ... chr18_gl000207_random >> 249250621 243199373 ... 4262 >> >>> tx<- transcripts(txdb, columns=c("tx_id", "tx_name", "gene_id")) >>> tx # a GRanges object with 1 transcript per row >>> >> GRangeswith 38098 ranges and 3 elementMetadata values >> seqnames ranges strand | tx_id tx_name >> <rle> <iranges> <rle> |<integer> <character> >> [1] chr1 [ 69091, 70008] + | 1021 NM_001005484 >> [2] chr1 [323892, 328581] + | 1023 NR_028327 >> [3] chr1 [323892, 328581] + | 1024 NR_028322 >> [4] chr1 [323892, 328581] + | 1025 NR_028325 >> [5] chr1 [367659, 368597] + | 1022 NM_001005277 >> [6] chr1 [367659, 368597] + | 1026 NM_001005221 >> [7] chr1 [367659, 368597] + | 1027 NM_001005224 >> [8] chr1 [763064, 789740] + | 174 NR_015368 >> [9] chr1 [861121, 879961] + | 1035 NM_152486 >> ... ... ... ... ... ... ... >> [38090] chrY [27177050, 27198251] - | 18991 NM_004678 >> [38091] chrY [27177050, 27198251] - | 18992 NM_001002760 >> [38092] chrY [27177050, 27198251] - | 18993 NM_001002761 >> [38093] chrY [27209230, 27246039] - | 18994 NR_001525 >> [38094] chrY [27209230, 27246039] - | 18995 NR_002177 >> [38095] chrY [27209230, 27246039] - | 18996 NR_002178 >> [38096] chrY [27329790, 27330920] - | 18997 NR_001526 >> [38097] chrY [27329790, 27330920] - | 18998 NR_002179 >> [38098] chrY [27329790, 27330920] - | 18999 NR_002180 >> gene_id >> <compressedcharacterlist> >> [1] 79501 >> [2] 100133331 >> [3] 100132287 >> [4] 100132062 >> [5] 81399 >> [6] 729759 >> [7] 26683 >> [8] 643837 >> [9] 148398 >> ... ... >> [38090] 9083 >> [38091] 442867 >> [38092] 442868 >> [38093] 114761 >> [38094] 474150 >> [38095] 474149 >> [38096] 252949 >> [38097] 474152 >> [38098] 474151 >> seqlengths >> chr1 chr2 ... chr18_gl000207_random >> 249250621 243199373 ... 4262 >> >>> seqnames(mysnps)<- sub("ch", "chr", seqnames(mysnps)) >>> map<- as.matrix(findOverlaps(mysnps, tx)) >>> >> Message d'avis : >> In .local(query, subject, maxgap, minoverlap, type, select, ...) : >> No seqnames from the 'query' and 'subject' were identical >> > It looks like the seqnames in mysnps were not renamed to the 'chr' > prefix. Prior to running findOverlaps, check the seqnames in both > objects to make sure the ranges you are interested in mapping have > identical seqnames, > > > unique(seqnames(mysnps)) > [1] chr1 unknown > Levels: chr1 unknown > > > > unique(seqnames(tx)) > [1] chr1 chr10 chr11 > [4] chr12 chr13 chr14 > .... and many more. > > Both objects have 'chr1' and when we run findOverlaps, > > > map<- as.matrix(findOverlaps(mysnps, tx)) > Warning message: > In .local(query, subject, maxgap, minoverlap, type, select, ...) : > Only some seqnames from 'query' and 'subject' were not identical > > This warning makes sense because mysnps only has 'chr1' and 'unknown' to > map to tx but there are many more seqnames in tx. Additionally, tx does > not have an 'unknown' seqname. > > > map > query subject > [1,] 1 49 > [2,] 2 1944 > [3,] 3 62 > [4,] 3 63 > [5,] 4 67 > > > >>> mapExon<- as.matrix(findOverlaps(mysnps, txExon)) >>> >> Message d'avis : >> In .local(query, subject, maxgap, minoverlap, type, select, ...) : >> No seqnames from the 'query' and 'subject' were identical >> >>> mapped_genes<- values(tx)$gene_id[map[, 2]] >>> mapped_snps<- rep.int(values(mysnps)$RefSNP_id[map[, 1]], >>> >> elementLengths(mapped_genes)) >> >>> snp2gene<- unique(data.frame(snp_id=mapped_snps, >>> >> gene_id=unlist(mapped_genes))) >> >>> rownames(snp2gene)<- NULL >>> snp2gene[1:4, ] >>> >> snp_id gene_id >> NA<na> <na> >> NA.1<na> <na> >> NA.2<na> <na> >> NA.3<na> <na> >> >> On our super computer, I can't update manualy the package. They >> are suposed to update automatically once per month according to our >> informactician. The result of sessionInfo() is : >> >> >>> sessionInfo() >>> >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-pc-linux-gnu (64-bit) >> locale: >> [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 >> [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C >> attachedbase packages: >> [1] stats graphics grDevices utils datasets methods base >> otherattached packages: >> [1] GenomicFeatures_1.2.3 >> [2] SNPlocs.Hsapiens.dbSNP.20101109_0.99.2 >> [3] GenomicRanges_1.2.2 >> [4] IRanges_1.8.7 >> loadedvia a namespace (and not attached): >> [1] Biobase_2.10.0 biomaRt_2.6.0 Biostrings_2.18.2 BSgenome_1.18.2 >> [5] DBI_0.2-5 RCurl_1.5-0 >> RSQLite_0.9-4 rtracklayer_1.10.6 >> [9] tools_2.12.0 XML_3.2-0 >> >> On my computer , something stragge happen. The >> package get unstalled when I run >> | source("http://bioconductor.org/biocLite.R") >> update.packages(repos=biocinstallRepos(), ask=FALSE, checkBuilt=TRUE) >> | >> >> And when I try to reinstall SNPlocs.Hsapiens.dbSNP.20101109, I now get >> an error message... >> >> >>> source("http://www.bioconductor.org/biocLite.R") >>> >> BioC_mirror= http://www.bioconductor.org >> Change using chooseBioCmirror(). >> >>> biocLite("SNPlocs.Hsapiens.dbSNP.20101109") >>> >> Using R version 2.12.0, biocinstall version 2.7.4. >> InstallingBioconductor version 2.7 packages: >> [1] "SNPlocs.Hsapiens.dbSNP.20101109" >> Pleasewait... >> Message d'avis : >> In getDependencies(pkgs, dependencies, available, lib) : >> package ?SNPlocs.Hsapiens.dbSNP.20101109? is not available >> >> >> >> >> >> >> >> But for sessionInfo, it's : >> >> >> >> >>> sessionInfo() >>> >> R version 2.12.0 (2010-10-15) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> locale: >> [1] LC_COLLATE=French_Canada.1252 LC_CTYPE=French_Canada.1252 >> [3] LC_MONETARY=French_Canada.1252 LC_NUMERIC=C >> [5] LC_TIME=French_Canada.1252 >> >> attachedbase packages: >> [1] stats graphics grDevices utils datasets methods base >> >> otherattached packages: >> [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2 IRanges_1.8.8 >> >> loadedvia a namespace (and not attached): >> [1] Biobase_2.10.0 biomaRt_2.6.0 Biostrings_2.18.2 BSgenome_1.18.2 >> >> [5] DBI_0.2-5 RCurl_1.5-0.1 RSQLite_0.9-4 >> rtracklayer_1.10.6 >> [9] XML_3.2-0.2 >> >> >> >> Now I have a super computer that can't run the program because of >> a subscript out of bounds and a personal computer than have a missing >> library... So now nothing work:( Other problem : why when >> I install again IRanges I got a version older than your for exemple? >> > The code should run on the linux machine (super computer) once you > address the seqnames problem above. You are having a problem installing > SNPlocs.Hsapiens.dbSNP.20101109 on your Windows pc because a Windows > binary of this package is not currently available. We should have this > available and I will let you know as soon as it is ready. Sorry about that. > > I had a newer version of IRanges in my last email because I was using > R-2.13, the devel branch. When using R-2.12 I have, > > >> sessionInfo() >> > R version 2.12.0 Patched (2010-10-18 r53360) > 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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicFeatures_1.2.3 > [2] SNPlocs.Hsapiens.dbSNP.20101109_0.99.2 > [3] GenomicRanges_1.2.2 > [4] IRanges_1.8.8 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 biomaRt_2.6.0 Biostrings_2.18.2 > BSgenome_1.18.2 > [5] DBI_0.2-5 RCurl_1.5-0 RSQLite_0.9-4 > rtracklayer_1.10.6 > [9] tools_2.12.0 XML_3.2-0 > > Valerie > >> >> Simon No?l >> CdeC >> > > [[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