SNPtools: Accessing, subsetting and plotting mouse SNPs.

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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.

Author
Daniel Gatti
Date of publication
2013-07-03 14:07:14
Maintainer
Daniel Gatti <Dan.Gatti@jax.org>
License
GPL-3
Version
1.1

View on CRAN

Man pages

categorize.variants
categorize.variants
cluster.strains
cluster.strains
convert.variants.to.GRanges
convert.variants.to.GRanges
convert.variants.to.numeric
convert.variants.to.numeric
example.genes
example.genes
example.snps
example.snps
find.overlapping.genes
find.overlapping.genes
gene.plot
gene.plot
get.mgi.features
get.mgi.features
get.pattern.variants
get.pattern.variants
get.strains
get.strains
get.variants
get.variants
qtl
qtl
snp.plot
snp.plot
SNPtools-internal
Accessing, subsetting and plotting mouse SNPs.
SNPtools-package
Accessing, subsetting and plotting mouse SNPs.
variant.plot
variant.plot

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