Question: Strange output in GenABEL convert.snp.ped()
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gravatar for Paul Geeleher
9.8 years ago by
Paul Geeleher1.3k
Paul Geeleher1.3k wrote:
Hi, I'm loading HapMap III data from here: ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_for mat/ Basically my code is as follows: setwd('/where/ped/and/map/files/are/') convert.snp.ped(ped='hapmap3_r2_b36_fwd.CEU.qc.poly.ped', map='hapmap3_r2_b36_fwd.CEU.qc.poly.map', out='ceu.out') hap3data <- load.gwaa.data(phenofile = "hapmap_CEU.ph", genofile = "ceu.out") The thing is if I look for the genotype information of a random SNP as follows: as.genotype(hap3data[, "rs9976865"]@gtdata) The output does NOT match up with what I'm seeing on the Hapmap website: http://hapmap.ncbi.nlm.nih.gov/cgi- perl/gbrowse/hapmap3r2_B36/ If I search for the SNP here the nucleotides seem to be different and they are not changing in the same way (I mean one of mine might be A/C and there might be an A/A on the hapmap site). From the "Reports & Analysis" drop down menu I'm selecting "Download SNP genotype data" and pressing "Go" to get this information. Any ideas what might be going wrong here? Thanks, Paul. -- Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com
snp hapmap • 709 views
ADD COMMENTlink modified 9.8 years ago by Martin Morgan ♦♦ 24k • written 9.8 years ago by Paul Geeleher1.3k
Answer: Strange output in GenABEL convert.snp.ped()
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gravatar for Martin Morgan
9.8 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
On 02/10/2010 05:36 AM, Paul Geeleher wrote: > Hi, > > I'm loading HapMap III data from here: > ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_f ormat/ Hi Paul -- Others might offer more helpful advice, but since GenABEL is not a Bioconductor package; have you tried contacting the maintainer? packageDescription("genABEL") Martin > > Basically my code is as follows: > > setwd('/where/ped/and/map/files/are/') > convert.snp.ped(ped='hapmap3_r2_b36_fwd.CEU.qc.poly.ped', > map='hapmap3_r2_b36_fwd.CEU.qc.poly.map', out='ceu.out') > hap3data <- load.gwaa.data(phenofile = "hapmap_CEU.ph", genofile = "ceu.out") > > The thing is if I look for the genotype information of a random SNP as follows: > > as.genotype(hap3data[, "rs9976865"]@gtdata) > > The output does NOT match up with what I'm seeing on the Hapmap > website: http://hapmap.ncbi.nlm.nih.gov/cgi- perl/gbrowse/hapmap3r2_B36/ > > If I search for the SNP here the nucleotides seem to be different and > they are not changing in the same way (I mean one of mine might be A/C > and there might be an A/A on the hapmap site). From the "Reports & > Analysis" drop down menu I'm selecting "Download SNP genotype data" > and pressing "Go" to get this information. > > Any ideas what might be going wrong here? > > Thanks, > > Paul. > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENTlink written 9.8 years ago by Martin Morgan ♦♦ 24k
Whoops, apologies, I was sure it was a bioconductor package! I'll follow your advice indeed. Paul On Wed, Feb 10, 2010 at 2:10 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 02/10/2010 05:36 AM, Paul Geeleher wrote: >> Hi, >> >> I'm loading HapMap III data from here: >> ftp://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/2009-01_phaseIII/plink_ format/ > > Hi Paul -- Others might offer more helpful advice, but since GenABEL is > not a Bioconductor package; have you tried contacting the maintainer? > > ?packageDescription("genABEL") > > Martin > >> >> Basically my code is as follows: >> >> setwd('/where/ped/and/map/files/are/') >> convert.snp.ped(ped='hapmap3_r2_b36_fwd.CEU.qc.poly.ped', >> map='hapmap3_r2_b36_fwd.CEU.qc.poly.map', out='ceu.out') >> hap3data <- load.gwaa.data(phenofile = "hapmap_CEU.ph", genofile = "ceu.out") >> >> The thing is if I look for the genotype information of a random SNP as follows: >> >> as.genotype(hap3data[, "rs9976865"]@gtdata) >> >> The output does NOT match up with what I'm seeing on the Hapmap >> website: http://hapmap.ncbi.nlm.nih.gov/cgi- perl/gbrowse/hapmap3r2_B36/ >> >> If I search for the SNP here the nucleotides seem to be different and >> they are not changing in the same way (I mean one of mine might be A/C >> and there might be an A/A on the hapmap site). From the "Reports & >> Analysis" drop down menu I'm selecting "Download SNP genotype data" >> and pressing "Go" to get this information. >> >> Any ideas what might be going wrong here? >> >> Thanks, >> >> Paul. >> > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > -- Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com
ADD REPLYlink written 9.8 years ago by Paul Geeleher1.3k
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