Genotype imputation
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@antoni-picornell-3780
Last seen 7.0 years ago
Hello, I am trying to impute genomic data in one case-control study with 2000 patients (1000+1000) and Illumina 1M. I need to perform 2 tasks: 1. Impute missing values in this 1Mx2000 matrix 2. Impute complete genotypes for a list of SNPs that are not in our platform. As far as I know, this can be done with non-R programs such as impute, mach, beagle or even plink (with poor results in this last case). In R we have the package GeneABEL, which could be useful in order to obtain the mach input from illumina data. Does anybody knows if there is some package in R that performs these kinds of tasks? How do you deal with this issue (even using non-R programs)? Thanks, Antoni Picornell
impute impute • 1.5k views
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Tim Rayner ▴ 270
@tim-rayner-2913
Last seen 7.0 years ago
Hi Antoni, I've been using the snpMatrix package for imputing SNPs which are not present on our platform. There's a convenient package vignette to walk you through the procedure. I've not tried imputing missing values, so I can't comment on that. Regards, Tim Rayner -- Bioinformatician Smith Lab, CIMR University of Cambridge 2009/11/5 Antoni Picornell <urnenfelder at="" gmail.com="">: > Hello, > > I am trying to impute genomic data in one case-control study with 2000 > patients (1000+1000) and Illumina 1M. > > I need to perform 2 tasks: > 1. Impute missing values in this 1Mx2000 matrix > 2. Impute complete genotypes for a list of SNPs that are not in our platform. > > As far as I know, this can be done with non-R programs such as impute, mach, > beagle or even plink (with poor results in this last case). In R we have the > package GeneABEL, which could be useful in order to obtain the mach input from > illumina data. > > Does anybody knows if there is some package in R that performs these kinds of > tasks? How do you deal with this issue (even using non-R programs)? > > Thanks, > Antoni Picornell > > _______________________________________________ > 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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Hi Tim, Thanks a lot for this suggestion. I'm already parsing my inputs in order to try it. Regards, Antoni. > Hi Antoni, > > I've been using the snpMatrix package for imputing SNPs which are not > present on our platform. There's a convenient package vignette to walk > you through the procedure. I've not tried imputing missing values, so > I can't comment on that. > > Regards, > > Tim Rayner > > -- > Bioinformatician > Smith Lab, CIMR > University of Cambridge > > 2009/11/5 Antoni Picornell <urnenfelder at="" gmail.com="">: > > Hello, > > > > I am trying to impute genomic data in one case-control study with 2000 > > patients (1000+1000) and Illumina 1M. > > > > I need to perform 2 tasks: > > 1. Impute missing values in this 1Mx2000 matrix > > 2. Impute complete genotypes for a list of SNPs that are not in our > > platform. > > > > As far as I know, this can be done with non-R programs such as impute, > > mach, beagle or even plink (with poor results in this last case). In R we > > have the package GeneABEL, which could be useful in order to obtain the > > mach input from illumina data. > > > > Does anybody knows if there is some package in R that performs these > > kinds of tasks? How do you deal with this issue (even using non-R > > programs)? > > > > Thanks, > > Antoni Picornell > > > > _______________________________________________ > > 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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