SNPtools: Accessing, subsetting and plotting mouse SNPs.
Version 1.1

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SNPtools")

Getting started

Package overview

Popular man pages

categorize.variants: categorize.variants
cluster.strains: cluster.strains
convert.variants.to.GRanges: convert.variants.to.GRanges
get.strains: get.strains
qtl: qtl
snp.plot: snp.plot
SNPtools-internal: Accessing, subsetting and plotting mouse SNPs.
See all...

All man pages Function index File listing

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

Functions

SNPmanipulation Man page
SNPmanipulation-package Man page
categorize.variants Man page Source code
check.args Man page Source code
cluster.strains Man page Source code
convert.genes.to.GRanges Source code
convert.pos.to.GRanges Man page Source code
convert.pos.to.bp Man page Source code
convert.variants.to.GRanges Man page Source code
convert.variants.to.numeric Man page Source code
create.pos Man page Source code
example.genes Man page
example.snps Man page
find.overlapping.genes Man page Source code
gene.plot Man page Source code
get.gene.name Source code
get.mgi.features Man page Source code
get.pattern.variants Man page Source code
get.strains Man page Source code
get.variants Man page Source code
line.up.genes Source code
qtl Man page
resolve.collisions Source code
snp.plot Man page Source code
strip.quality.columns Source code
variant.plot Man page Source code

Files

MD5
vignettes
vignettes/SNPtools.Rnw
test
test/SNPtools.tests.R
man
man/variant.plot.Rd
man/snp.plot.Rd
man/qtl.Rd
man/get.variants.Rd
man/get.strains.Rd
man/get.pattern.variants.Rd
man/get.mgi.features.Rd
man/gene.plot.Rd
man/find.overlapping.genes.Rd
man/example.snps.Rd
man/example.genes.Rd
man/convert.variants.to.numeric.Rd
man/convert.variants.to.GRanges.Rd
man/cluster.strains.Rd
man/categorize.variants.Rd
man/SNPtools-package.Rd
man/SNPtools-internal.Rd
inst
inst/doc
inst/doc/SNPtools.pdf
inst/doc/SNPtools.Rnw
inst/doc/SNPtools.R
data
data/qtl.rda
data/example.snps.rda
data/example.genes.rda
R
R/variant.plot.R
R/strip.quality.columns.R
R/snp.manipulation-internal.R
R/get.variants.R
R/get.strains.R
R/get.pattern.variants.R
R/get.mgi.features.R
R/gene.plot.R
R/find.overlapping.genes.R
R/create.pos.R
R/convert.variants.to.numeric.R
R/convert.variants.to.GRanges.R
R/convert.pos.to.bp.R
R/convert.pos.to.GRanges.R
R/convert.genes.to.GRanges.R
R/cluster.strains.R
R/check.args.R
R/categorize.variants.R
NAMESPACE
DESCRIPTION
SNPtools documentation built on May 19, 2017, 1 p.m.

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

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.