Distinguish Synonymous vs. Non-synonymous SNPs
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Wu, Xiwei ▴ 350
@wu-xiwei-1102
Last seen 10.2 years ago
Dear list, I have a list of SNPs with chromosome location, and trying to see which ones are non-synonymous. Are there any packages/functions that can distinguish synonymous and non-synonymous SNPs? I tried to search the list, but could not find anything related. Thanks in advance. Xiwei --------------------------------------------------------------------- SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:30}}
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@michael-dondrup-3849
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Hi Xiwei, do you mean SNPs that result in non-synonymous vs synonymous coding? Then a biomart query might do the job and therefore the package biomaRt could be used to query from within R. There is a filter in biomart for different consequence types of SNPs, one of which is NON_SYNONYMOUS_CODING. You can check which filter seems appropriate This lengthy Url represents a possible query in the biomart web interface: http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTR IBUTES=hsapiens_snp.default.snp.refsnp_id|hsapiens_snp.default.snp.chr _name|hsapiens_snp.default.snp.chrom_start|hsapiens_snp.default.snp.co nsequence_type_tv|hsapiens_snp.default.snp.ensembl_type|hsapiens_snp.d efault.snp.ensembl_peptide_shift|hsapiens_snp.default.snp.phenotype_de scription|hsapiens_snp.default.snp.phenotype_name&FILTERS=hsapiens_snp .default.filters.consequence_type."NON_SYNONYMOUS_CODING"&VISIBLEPANEL =resultspanel it should be possible to set identical parameters in the bioconductor package biomaRt although I didn't try this yet. Best Michael Am Jan 29, 2010 um 1:57 AM schrieb Wu, Xiwei: > Dear list, > > I have a list of SNPs with chromosome location, and trying to see which > ones are non-synonymous. Are there any packages/functions that can > distinguish synonymous and non-synonymous SNPs? I tried to search the > list, but could not find anything related. Thanks in advance. > > Xiwei > > > > > --------------------------------------------------------------------- > SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:30}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Michael, Thanks a lot for your help. I will give it a try. Is it good for novel SNPs not in the dbSNP? The SNPs I got are from a sequencing project, many of them are not in dbSNP. Xiwei -----Original Message----- From: Michael Dondrup [mailto:Michael.Dondrup@uni.no] Sent: Friday, January 29, 2010 3:11 AM To: Wu, Xiwei Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Distinguish Synonymous vs. Non-synonymous SNPs Hi Xiwei, do you mean SNPs that result in non-synonymous vs synonymous coding? Then a biomart query might do the job and therefore the package biomaRt could be used to query from within R. There is a filter in biomart for different consequence types of SNPs, one of which is NON_SYNONYMOUS_CODING. You can check which filter seems appropriate This lengthy Url represents a possible query in the biomart web interface: http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTR IB UTES=hsapiens_snp.default.snp.refsnp_id|hsapiens_snp.default.snp.chr_n am e|hsapiens_snp.default.snp.chrom_start|hsapiens_snp.default.snp.conseq ue nce_type_tv|hsapiens_snp.default.snp.ensembl_type|hsapiens_snp.default .s np.ensembl_peptide_shift|hsapiens_snp.default.snp.phenotype_descriptio n| hsapiens_snp.default.snp.phenotype_name&FILTERS=hsapiens_snp.default.f il ters.consequence_type."NON_SYNONYMOUS_CODING"&VISIBLEPANEL=resultspane l it should be possible to set identical parameters in the bioconductor package biomaRt although I didn't try this yet. Best Michael Am Jan 29, 2010 um 1:57 AM schrieb Wu, Xiwei: > Dear list, > > I have a list of SNPs with chromosome location, and trying to see which > ones are non-synonymous. Are there any packages/functions that can > distinguish synonymous and non-synonymous SNPs? I tried to search the > list, but could not find anything related. Thanks in advance. > > Xiwei > > > > > --------------------------------------------------------------------- > SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:30}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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I'm not sure BioC is the tool you want to use. Have you tried something like BioPerl: http://www.bioperl.org/Core/Latest/bioscripts.html#scripts_utilities_p airwise_kaks_pls "Takes DNA sequences as input, aligns them as proteins, projects the alignment back into DNA and estimates the Ka (non-synonymous) and Ks (synonymous) substitutions." ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Wu, Xiwei [XWu@coh.org] Sent: 29 January 2010 17:26 To: Michael Dondrup Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Distinguish Synonymous vs. Non-synonymous SNPs Michael, Thanks a lot for your help. I will give it a try. Is it good for novel SNPs not in the dbSNP? The SNPs I got are from a sequencing project, many of them are not in dbSNP. Xiwei -----Original Message----- From: Michael Dondrup [mailto:Michael.Dondrup@uni.no] Sent: Friday, January 29, 2010 3:11 AM To: Wu, Xiwei Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Distinguish Synonymous vs. Non-synonymous SNPs Hi Xiwei, do you mean SNPs that result in non-synonymous vs synonymous coding? Then a biomart query might do the job and therefore the package biomaRt could be used to query from within R. There is a filter in biomart for different consequence types of SNPs, one of which is NON_SYNONYMOUS_CODING. You can check which filter seems appropriate This lengthy Url represents a possible query in the biomart web interface: http://www.biomart.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTR IB UTES=hsapiens_snp.default.snp.refsnp_id|hsapiens_snp.default.snp.chr_n am e|hsapiens_snp.default.snp.chrom_start|hsapiens_snp.default.snp.conseq ue nce_type_tv|hsapiens_snp.default.snp.ensembl_type|hsapiens_snp.default .s np.ensembl_peptide_shift|hsapiens_snp.default.snp.phenotype_descriptio n| hsapiens_snp.default.snp.phenotype_name&FILTERS=hsapiens_snp.default.f il ters.consequence_type."NON_SYNONYMOUS_CODING"&VISIBLEPANEL=resultspane l it should be possible to set identical parameters in the bioconductor package biomaRt although I didn't try this yet. Best Michael Am Jan 29, 2010 um 1:57 AM schrieb Wu, Xiwei: > Dear list, > > I have a list of SNPs with chromosome location, and trying to see which > ones are non-synonymous. Are there any packages/functions that can > distinguish synonymous and non-synonymous SNPs? I tried to search the > list, but could not find anything related. Thanks in advance. > > Xiwei > > > > > --------------------------------------------------------------------- > SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:30}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dear all, I found that the findOverlaps function does not work properly if the space levels do not match exactly between subject and query. Has anyone noticed the same problem? I am using the R-2.10.0 and IRanges-1.4.0. Is this problem being fixed in the developmental version? Thanks. Xiwei --------------------------------------------------------------------- SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:30}}
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Need input... what is the expected result? and what actually happened? sessionInfo()... On Fri, Jan 29, 2010 at 11:47 AM, Wu, Xiwei <xwu@coh.org> wrote: > Dear all, > > I found that the findOverlaps function does not work properly if the > space levels do not match exactly between subject and query. Has anyone > noticed the same problem? I am using the R-2.10.0 and IRanges-1.4.0. Is > this problem being fixed in the developmental version? > > Thanks. > > Xiwei > > > --------------------------------------------------------------------- > SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:30}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > 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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Michael, Here is one example. Please let me know if I have missed anything. Thanks. > a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3, 7), sep="")) > b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5, 21, 3, "X"), sep="")) > as.matrix(findOverlaps(a, a)) query subject [1,] 1 1 [2,] 2 2 [3,] 3 3 [4,] 4 4 [5,] 5 5 [6,] 6 6 [7,] 7 7 > as.matrix(findOverlaps(a, b)) query subject [1,] 1 1 [2,] 2 3 [3,] 3 5 [4,] 4 5 > a[4] RangedData with 1 row and 0 value columns across 1 space space ranges | <character> <iranges> | 1 chr5 [1, 10] | > b[5] RangedData with 1 row and 0 value columns across 1 space space ranges | <character> <iranges> | 1 chr3 [1, 10] | > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu 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=C [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] rtracklayer_1.6.0 RCurl_1.3-1 [3] bitops_1.0-4.1 BSgenome.Hsapiens.UCSC.hg18_1.3.15 [5] ShortRead_1.4.0 lattice_0.17-26 [7] BSgenome_1.14.0 Biostrings_2.14.0 [9] IRanges_1.4.0 loaded via a namespace (and not attached): [1] Biobase_2.6.0 grid_2.10.0 hwriter_1.1 tools_2.10.0 XML_2.6-0 Xiwei ________________________________________ From: Michael Lawrence [mailto:lawrence.michael@gene.com] Sent: Friday, January 29, 2010 1:13 PM To: Wu, Xiwei Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] FindOverlaps Problem Need input... what is the expected result? and what actually happened? sessionInfo()... On Fri, Jan 29, 2010 at 11:47 AM, Wu, Xiwei <xwu at="" coh.org=""> wrote: Dear all, I found that the findOverlaps function does not work properly if the space levels do not match exactly between subject and query. Has anyone noticed the same problem? I am using the R-2.10.0 and IRanges-1.4.0. Is this problem being fixed in the developmental version? Thanks. Xiwei --------------------------------------------------------------------- SECURITY/CONFIDENTIALITY WARNING: ?\ This message and ...{{dropped:10}}
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It seems to me that it is working correctly but you can't assume that the order of ranges at time of construction serves as the order in the ultimate object. A lexicographic ordering by space names is used. Challenging to interpret but if you look at the values of a and b before interpreting your findOverlaps result it starts to make sense. > a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3, 7), sep="")) > a RangedData with 7 rows and 0 value columns across 7 spaces space ranges | <character> <iranges> | 1 chr10 [1, 10] | 2 chr2 [1, 10] | 3 chr3 [1, 10] | 4 chr5 [1, 10] | 5 chr6 [1, 10] | 6 chr7 [1, 10] | 7 chr9 [1, 10] | > b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5, 21, 3 , "X"), sep="")) > b RangedData with 7 rows and 0 value columns across 7 spaces space ranges | <character> <iranges> | 1 chr10 [1, 10] | 2 chr18 [1, 10] | 3 chr2 [1, 10] | 4 chr21 [1, 10] | 5 chr3 [1, 10] | 6 chr5 [1, 10] | 7 chrX [1, 10] | > findOverlaps(a,b) RangesMatchingList of length 7 names(7): chr10 chr2 chr3 chr5 chr6 chr7 chr9 > as.matrix(.Last.value) query subject [1,] 1 1 [2,] 2 3 [3,] 3 5 [4,] 4 6 On Sat, Jan 30, 2010 at 1:09 PM, Wu, Xiwei <xwu at="" coh.org=""> wrote: > Michael, > > Here is one example. Please let me know if I have missed anything. Thanks. > >> a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3, 7), sep="")) >> b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5, 21, 3, "X"), sep="")) >> as.matrix(findOverlaps(a, a)) > ? ? query subject > [1,] ? ? 1 ? ? ? 1 > [2,] ? ? 2 ? ? ? 2 > [3,] ? ? 3 ? ? ? 3 > [4,] ? ? 4 ? ? ? 4 > [5,] ? ? 5 ? ? ? 5 > [6,] ? ? 6 ? ? ? 6 > [7,] ? ? 7 ? ? ? 7 >> as.matrix(findOverlaps(a, b)) > ? ? query subject > [1,] ? ? 1 ? ? ? 1 > [2,] ? ? 2 ? ? ? 3 > [3,] ? ? 3 ? ? ? 5 > [4,] ? ? 4 ? ? ? 5 >> a[4] > RangedData with 1 row and 0 value columns across 1 space > ? ? ? ?space ? ?ranges | > ?<character> <iranges> | > 1 ? ? ? ?chr5 ? [1, 10] | >> b[5] > RangedData with 1 row and 0 value columns across 1 space > ? ? ? ?space ? ?ranges | > ?<character> <iranges> | > 1 ? ? ? ?chr3 ? [1, 10] | >> sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-unknown-linux-gnu > > 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=C > ?[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] rtracklayer_1.6.0 ? ? ? ? ? ? ? ? ?RCurl_1.3-1 > [3] bitops_1.0-4.1 ? ? ? ? ? ? ? ? ? ? BSgenome.Hsapiens.UCSC.hg18_1.3.15 > [5] ShortRead_1.4.0 ? ? ? ? ? ? ? ? ? ?lattice_0.17-26 > [7] BSgenome_1.14.0 ? ? ? ? ? ? ? ? ? ?Biostrings_2.14.0 > [9] IRanges_1.4.0 > > loaded via a namespace (and not attached): > [1] Biobase_2.6.0 grid_2.10.0 ? hwriter_1.1 ? tools_2.10.0 ?XML_2.6-0 > > > Xiwei > ________________________________________ > From: Michael Lawrence [mailto:lawrence.michael at gene.com] > Sent: Friday, January 29, 2010 1:13 PM > To: Wu, Xiwei > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] FindOverlaps Problem > > Need input... what is the expected result? and what actually happened? sessionInfo()... > On Fri, Jan 29, 2010 at 11:47 AM, Wu, Xiwei <xwu at="" coh.org=""> wrote: > Dear all, > > I found that the findOverlaps function does not work properly if the > space levels do not match exactly between subject and query. Has anyone > noticed the same problem? I am using the R-2.10.0 and IRanges-1.4.0. Is > this problem being fixed in the developmental version? > > Thanks. > > Xiwei > > > --------------------------------------------------------------------- > SECURITY/CONFIDENTIALITY WARNING: ?\ This message and ...{{dropped:10}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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ah -- my result was with devel, and in fact it does not agree with yours, but it seems correct in this instance. > sessionInfo() R version 2.11.0 Under development (unstable) (2010-01-07 r50940) i386-apple-darwin9.8.0 locale: [1] C attached base packages: [1] grid stats graphics grDevices datasets tools utils [8] methods base other attached packages: [1] GenomeGraphs_1.7.1 biomaRt_2.3.0 leeBamSet_0.0.8 [4] Rsamtools_0.1.24 BSgenome_1.15.4 Biostrings_2.15.18 [7] IRanges_1.5.31 org.Sc.sgd.db_2.3.5 RSQLite_0.7-3 [10] DBI_0.2-4 AnnotationDbi_1.9.0 Biobase_2.7.0 [13] weaver_1.13.0 codetools_0.2-2 digest_0.4.1 loaded via a namespace (and not attached): [1] RCurl_1.3-0 XML_2.6-0 On Sat, Jan 30, 2010 at 4:30 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > It seems to me that it is working correctly but you can't assume that > the order of ranges at time of construction serves as the order in the > ultimate object. ?A lexicographic ordering by space names is used. > Challenging to interpret but if you look at the values of a and b > before interpreting your findOverlaps result it starts to make sense. > >> a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3, > 7), sep="")) >> a > RangedData with 7 rows and 0 value columns across 7 spaces > ? ? ? ?space ? ?ranges | > ?<character> <iranges> | > 1 ? ? ? chr10 ? [1, 10] | > 2 ? ? ? ?chr2 ? [1, 10] | > 3 ? ? ? ?chr3 ? [1, 10] | > 4 ? ? ? ?chr5 ? [1, 10] | > 5 ? ? ? ?chr6 ? [1, 10] | > 6 ? ? ? ?chr7 ? [1, 10] | > 7 ? ? ? ?chr9 ? [1, 10] | >> b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5, 21, 3 > , "X"), sep="")) >> b > RangedData with 7 rows and 0 value columns across 7 spaces > ? ? ? ?space ? ?ranges | > ?<character> <iranges> | > 1 ? ? ? chr10 ? [1, 10] | > 2 ? ? ? chr18 ? [1, 10] | > 3 ? ? ? ?chr2 ? [1, 10] | > 4 ? ? ? chr21 ? [1, 10] | > 5 ? ? ? ?chr3 ? [1, 10] | > 6 ? ? ? ?chr5 ? [1, 10] | > 7 ? ? ? ?chrX ? [1, 10] | >> findOverlaps(a,b) > RangesMatchingList of length 7 > names(7): chr10 chr2 chr3 chr5 chr6 chr7 chr9 >> as.matrix(.Last.value) > ? ? query subject > [1,] ? ? 1 ? ? ? 1 > [2,] ? ? 2 ? ? ? 3 > [3,] ? ? 3 ? ? ? 5 > [4,] ? ? 4 ? ? ? 6 > > > On Sat, Jan 30, 2010 at 1:09 PM, Wu, Xiwei <xwu at="" coh.org=""> wrote: >> Michael, >> >> Here is one example. Please let me know if I have missed anything. Thanks. >> >>> a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 9, 5, 6, 3, 7), sep="")) >>> b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), space=paste("chr", c(2, 10, 18, 5, 21, 3, "X"), sep="")) >>> as.matrix(findOverlaps(a, a)) >> ? ? query subject >> [1,] ? ? 1 ? ? ? 1 >> [2,] ? ? 2 ? ? ? 2 >> [3,] ? ? 3 ? ? ? 3 >> [4,] ? ? 4 ? ? ? 4 >> [5,] ? ? 5 ? ? ? 5 >> [6,] ? ? 6 ? ? ? 6 >> [7,] ? ? 7 ? ? ? 7 >>> as.matrix(findOverlaps(a, b)) >> ? ? query subject >> [1,] ? ? 1 ? ? ? 1 >> [2,] ? ? 2 ? ? ? 3 >> [3,] ? ? 3 ? ? ? 5 >> [4,] ? ? 4 ? ? ? 5 >>> a[4] >> RangedData with 1 row and 0 value columns across 1 space >> ? ? ? ?space ? ?ranges | >> ?<character> <iranges> | >> 1 ? ? ? ?chr5 ? [1, 10] | >>> b[5] >> RangedData with 1 row and 0 value columns across 1 space >> ? ? ? ?space ? ?ranges | >> ?<character> <iranges> | >> 1 ? ? ? ?chr3 ? [1, 10] | >>> sessionInfo() >> R version 2.10.0 (2009-10-26) >> x86_64-unknown-linux-gnu >> >> 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=C >> ?[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] rtracklayer_1.6.0 ? ? ? ? ? ? ? ? ?RCurl_1.3-1 >> [3] bitops_1.0-4.1 ? ? ? ? ? ? ? ? ? ? BSgenome.Hsapiens.UCSC.hg18_1.3.15 >> [5] ShortRead_1.4.0 ? ? ? ? ? ? ? ? ? ?lattice_0.17-26 >> [7] BSgenome_1.14.0 ? ? ? ? ? ? ? ? ? ?Biostrings_2.14.0 >> [9] IRanges_1.4.0 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.6.0 grid_2.10.0 ? hwriter_1.1 ? tools_2.10.0 ?XML_2.6-0 >> >> >> Xiwei >> ________________________________________ >> From: Michael Lawrence [mailto:lawrence.michael at gene.com] >> Sent: Friday, January 29, 2010 1:13 PM >> To: Wu, Xiwei >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] FindOverlaps Problem >> >> Need input... what is the expected result? and what actually happened? sessionInfo()... >> On Fri, Jan 29, 2010 at 11:47 AM, Wu, Xiwei <xwu at="" coh.org=""> wrote: >> Dear all, >> >> I found that the findOverlaps function does not work properly if the >> space levels do not match exactly between subject and query. Has anyone >> noticed the same problem? I am using the R-2.10.0 and IRanges-1.4.0. Is >> this problem being fixed in the developmental version? >> >> Thanks. >> >> Xiwei >> >> >> --------------------------------------------------------------------- >> SECURITY/CONFIDENTIALITY WARNING: ?\ This message and ...{{dropped:10}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
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On Sat, Jan 30, 2010 at 1:33 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > ah -- my result was with devel, and in fact it does not agree with > yours, but it seems correct in this instance. > > I think there was a bug in the as.matrix() method on the overlap result that was fixed relatively recently. This probably explains the difference. Thanks for looking into this Vince. Michael > > sessionInfo() > R version 2.11.0 Under development (unstable) (2010-01-07 r50940) > i386-apple-darwin9.8.0 > > locale: > [1] C > > attached base packages: > [1] grid stats graphics grDevices datasets tools utils > [8] methods base > > other attached packages: > [1] GenomeGraphs_1.7.1 biomaRt_2.3.0 leeBamSet_0.0.8 > [4] Rsamtools_0.1.24 BSgenome_1.15.4 Biostrings_2.15.18 > [7] IRanges_1.5.31 org.Sc.sgd.db_2.3.5 RSQLite_0.7-3 > [10] DBI_0.2-4 AnnotationDbi_1.9.0 Biobase_2.7.0 > [13] weaver_1.13.0 codetools_0.2-2 digest_0.4.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.3-0 XML_2.6-0 > > > On Sat, Jan 30, 2010 at 4:30 PM, Vincent Carey > <stvjc@channing.harvard.edu> wrote: > > It seems to me that it is working correctly but you can't assume that > > the order of ranges at time of construction serves as the order in the > > ultimate object. A lexicographic ordering by space names is used. > > Challenging to interpret but if you look at the values of a and b > > before interpreting your findOverlaps result it starts to make sense. > > > >> a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), > space=paste("chr", c(2, 10, 9, 5, 6, 3, > > 7), sep="")) > >> a > > RangedData with 7 rows and 0 value columns across 7 spaces > > space ranges | > > <character> <iranges> | > > 1 chr10 [1, 10] | > > 2 chr2 [1, 10] | > > 3 chr3 [1, 10] | > > 4 chr5 [1, 10] | > > 5 chr6 [1, 10] | > > 6 chr7 [1, 10] | > > 7 chr9 [1, 10] | > >> b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), > space=paste("chr", c(2, 10, 18, 5, 21, 3 > > , "X"), sep="")) > >> b > > RangedData with 7 rows and 0 value columns across 7 spaces > > space ranges | > > <character> <iranges> | > > 1 chr10 [1, 10] | > > 2 chr18 [1, 10] | > > 3 chr2 [1, 10] | > > 4 chr21 [1, 10] | > > 5 chr3 [1, 10] | > > 6 chr5 [1, 10] | > > 7 chrX [1, 10] | > >> findOverlaps(a,b) > > RangesMatchingList of length 7 > > names(7): chr10 chr2 chr3 chr5 chr6 chr7 chr9 > >> as.matrix(.Last.value) > > query subject > > [1,] 1 1 > > [2,] 2 3 > > [3,] 3 5 > > [4,] 4 6 > > > > > > On Sat, Jan 30, 2010 at 1:09 PM, Wu, Xiwei <xwu@coh.org> wrote: > >> Michael, > >> > >> Here is one example. Please let me know if I have missed anything. > Thanks. > >> > >>> a <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), > space=paste("chr", c(2, 10, 9, 5, 6, 3, 7), sep="")) > >>> b <- RangedData(IRanges(start=rep(1,7), end=rep(10,7)), > space=paste("chr", c(2, 10, 18, 5, 21, 3, "X"), sep="")) > >>> as.matrix(findOverlaps(a, a)) > >> query subject > >> [1,] 1 1 > >> [2,] 2 2 > >> [3,] 3 3 > >> [4,] 4 4 > >> [5,] 5 5 > >> [6,] 6 6 > >> [7,] 7 7 > >>> as.matrix(findOverlaps(a, b)) > >> query subject > >> [1,] 1 1 > >> [2,] 2 3 > >> [3,] 3 5 > >> [4,] 4 5 > >>> a[4] > >> RangedData with 1 row and 0 value columns across 1 space > >> space ranges | > >> <character> <iranges> | > >> 1 chr5 [1, 10] | > >>> b[5] > >> RangedData with 1 row and 0 value columns across 1 space > >> space ranges | > >> <character> <iranges> | > >> 1 chr3 [1, 10] | > >>> sessionInfo() > >> R version 2.10.0 (2009-10-26) > >> x86_64-unknown-linux-gnu > >> > >> 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=C > >> [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] rtracklayer_1.6.0 RCurl_1.3-1 > >> [3] bitops_1.0-4.1 > BSgenome.Hsapiens.UCSC.hg18_1.3.15 > >> [5] ShortRead_1.4.0 lattice_0.17-26 > >> [7] BSgenome_1.14.0 Biostrings_2.14.0 > >> [9] IRanges_1.4.0 > >> > >> loaded via a namespace (and not attached): > >> [1] Biobase_2.6.0 grid_2.10.0 hwriter_1.1 tools_2.10.0 XML_2.6-0 > >> > >> > >> Xiwei > >> ________________________________________ > >> From: Michael Lawrence [mailto:lawrence.michael@gene.com] > >> Sent: Friday, January 29, 2010 1:13 PM > >> To: Wu, Xiwei > >> Cc: bioconductor@stat.math.ethz.ch > >> Subject: Re: [BioC] FindOverlaps Problem > >> > >> Need input... what is the expected result? and what actually happened? > sessionInfo()... > >> On Fri, Jan 29, 2010 at 11:47 AM, Wu, Xiwei <xwu@coh.org> wrote: > >> Dear all, > >> > >> I found that the findOverlaps function does not work properly if the > >> space levels do not match exactly between subject and query. Has anyone > >> noticed the same problem? I am using the R-2.10.0 and IRanges-1.4.0. Is > >> this problem being fixed in the developmental version? > >> > >> Thanks. > >> > >> Xiwei > >> > >> > >> --------------------------------------------------------------------- > >> SECURITY/CONFIDENTIALITY WARNING: \ This message and ...{{dropped:10}} > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@stat.math.ethz.ch > >> 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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