scoreInvHap

DOI: 10.18129/B9.bioc.scoreInvHap    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see scoreInvHap.

Get inversion status in predefined regions

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scoreInvHap")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.6.0
In Bioconductor since	BioC 3.6 (R-3.4) (2 years)
License	file LICENSE
Depends	R (>= 3.4.0)
Imports	Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment
LinkingTo
Suggests	testthat, knitr, BiocStyle, rmarkdown
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Build Report

Package Archives

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

Source Package	scoreInvHap_1.6.0.tar.gz
Windows Binary	scoreInvHap_1.6.0.zip
Mac OS X 10.11 (El Capitan)	scoreInvHap_1.6.0.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	https://bioconductor.org/packages/scoreInvHap/
Package Downloads Report	Download Stats