This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

scoreInvHap

Get inversion status in predefined regions

Bioconductor version: Release (3.17)

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 21 inversions.

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

Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>

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

Installation

To install this package, start R (version "4.3") 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")
Inversion genotyping with scoreInvHap HTML R Script
Reference Manual PDF
LICENSE Text

Details

biocViews Genetics, GenomicVariation, SNP, Software
Version 1.22.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License file LICENSE
Depends R (>= 3.6.0)
Imports Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment
Linking To
Suggests testthat, knitr, BiocStyle, rmarkdown
System Requirements
Enhances
URL
See More
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_1.22.0.tar.gz
Windows Binary scoreInvHap_1.22.0.zip
macOS Binary (x86_64) scoreInvHap_1.22.0.tgz
macOS Binary (arm64) scoreInvHap_1.22.0.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