scoreInvHap

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see scoreInvHap.

Get inversion status in predefined regions


Bioconductor version: 3.10

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 (version "3.6") and enter:


if (!require("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")
Call haplotype inversions with scoreInvHap HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Genetics, GenomicVariation, SNP, Software
Version 1.8.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License file LICENSE
Depends R (>= 3.4.0)
Imports Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment
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Suggests testthat, knitr, BiocStyle, rmarkdown
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Package Archives

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

Source Package scoreInvHap_1.8.0.tar.gz
Windows Binary scoreInvHap_1.8.0.zip
Mac OS X 10.11 (El Capitan) scoreInvHap_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scoreInvHap
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scoreInvHap
Bioc Package Browser https://code.bioconductor.org/browse/scoreInvHap/
Package Short Url https://bioconductor.org/packages/scoreInvHap/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive