SNPmanipulation-package

SNPmanipulation


There are several large mouse SNP data sets (Sanger, MouseHapMap, Perlegen, UNC).  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 ploymorphic for a subset of strains, plot SNPs and look for certain allele pattens in 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.

SNPmanipulation-package: Accessing, subsetting and plotting mouse SNPs.

Description

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Details