SNPtools: Accessing, subsetting and plotting mouse SNPs.

This package queries the SNPs data sets and makes plots of genes and SNPs. This package allows users to access these data sets once they have been compiled into one file and indexed with Tabix (http://samtools.sourceforge.net/tabix.shtml). There are functions to retrieve SNPs, subset them for specific strains, obtain only SNPs that are polymorphic for a subset of strains, plot SNPs and look for certain allele patterns in SNPs. We have also added functions to access indels and structural variants.

AuthorDaniel Gatti
Date of publication2013-07-03 14:07:14
MaintainerDaniel Gatti <Dan.Gatti@jax.org>
LicenseGPL-3
Version1.1

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Files in this package

SNPtools
SNPtools/MD5
SNPtools/vignettes
SNPtools/vignettes/SNPtools.Rnw
SNPtools/test
SNPtools/test/SNPtools.tests.R
SNPtools/man
SNPtools/man/variant.plot.Rd SNPtools/man/snp.plot.Rd SNPtools/man/qtl.Rd SNPtools/man/get.variants.Rd SNPtools/man/get.strains.Rd SNPtools/man/get.pattern.variants.Rd SNPtools/man/get.mgi.features.Rd SNPtools/man/gene.plot.Rd SNPtools/man/find.overlapping.genes.Rd SNPtools/man/example.snps.Rd SNPtools/man/example.genes.Rd SNPtools/man/convert.variants.to.numeric.Rd SNPtools/man/convert.variants.to.GRanges.Rd SNPtools/man/cluster.strains.Rd SNPtools/man/categorize.variants.Rd SNPtools/man/SNPtools-package.Rd SNPtools/man/SNPtools-internal.Rd
SNPtools/inst
SNPtools/inst/doc
SNPtools/inst/doc/SNPtools.pdf
SNPtools/inst/doc/SNPtools.Rnw
SNPtools/inst/doc/SNPtools.R
SNPtools/data
SNPtools/data/qtl.rda
SNPtools/data/example.snps.rda
SNPtools/data/example.genes.rda
SNPtools/R
SNPtools/R/variant.plot.R SNPtools/R/strip.quality.columns.R SNPtools/R/snp.manipulation-internal.R SNPtools/R/get.variants.R SNPtools/R/get.strains.R SNPtools/R/get.pattern.variants.R SNPtools/R/get.mgi.features.R SNPtools/R/gene.plot.R SNPtools/R/find.overlapping.genes.R SNPtools/R/create.pos.R SNPtools/R/convert.variants.to.numeric.R SNPtools/R/convert.variants.to.GRanges.R SNPtools/R/convert.pos.to.bp.R SNPtools/R/convert.pos.to.GRanges.R SNPtools/R/convert.genes.to.GRanges.R SNPtools/R/cluster.strains.R SNPtools/R/check.args.R SNPtools/R/categorize.variants.R
SNPtools/NAMESPACE
SNPtools/DESCRIPTION

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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