scoreInvHap

DOI: 10.18129/B9.bioc.scoreInvHap    

Get inversion status in predefined regions

Bioconductor version: Release (3.7)

scoreInvHap can get the samples' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for two well known inversions (8p23 and 17q21.31) and for two additional regions.

Author: Carlos Ruiz [aut, cre], Juan R. Gonzalez [aut]

Maintainer: Carlos Ruiz <carlos.ruiz at isglobal.org>

Citation (from within R, enter citation("scoreInvHap")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("scoreInvHap")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scoreInvHap")

 

HTML R Script Call haplotype inversions with scoreInvHap
PDF   Reference Manual
Text   LICENSE

Details

biocViews Genetics, GenomicVariation, SNP, Software
Version 1.2.1
License file LICENSE
Depends R (>= 3.4.0)
Imports Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment
LinkingTo
Suggests testthat, knitr, BiocStyle, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scoreInvHap_1.2.1.tar.gz
Windows Binary scoreInvHap_1.2.1.zip
Mac OS X 10.11 (El Capitan) scoreInvHap_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/scoreInvHap
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scoreInvHap
Package Short Url http://bioconductor.org/packages/scoreInvHap/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: