To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

scoreInvHap

DOI: 10.18129/B9.bioc.scoreInvHap    

This is the development version of scoreInvHap; to use it, please install the devel version of Bioconductor.

Get inversion status in predefined regions

Bioconductor version: Development (3.6)

scoreInvHap can get the samples' inversion status of known inversions. SNPfier 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

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

Details

biocViews Genetics, GenomicVariation, SNP, Software
Version 0.99.17
In Bioconductor since BioC 3.6 (R-3.4)
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
Build Report  

Package Archives

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

Package Source scoreInvHap_0.99.17.tar.gz
Windows Binary scoreInvHap_0.99.17.zip
Mac OS X 10.11 (El Capitan) scoreInvHap_0.99.17.tgz
Source Repository git clone https://git.bioconductor.org/packages/scoreInvHap
Package Short Url http://bioconductor.org/packages/scoreInvHap/
Package Downloads Report Download Stats

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