scoreInvHap

This is the development version of scoreInvHap; for the stable release version, see scoreInvHap.

Get inversion status in predefined regions

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Genetics, GenomicVariation, SNP, Software
Version	1.31.0
In Bioconductor since	BioC 3.6 (R-3.4) (8 years)
License	file LICENSE
Depends	R (>= 3.6.0)
Imports	Biostrings, methods, snpStats, VariantAnnotation, GenomicRanges, BiocParallel, graphics, SummarizedExperiment
System Requirements
URL

Suggests	testthat, knitr, BiocStyle, rmarkdown
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Build Report	Build Report

Package Archives

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

Source Package	scoreInvHap_1.31.0.tar.gz
Windows Binary (x86_64)	scoreInvHap_1.31.0.zip
macOS Binary (x86_64)	scoreInvHap_1.31.0.tgz
macOS Binary (arm64)	scoreInvHap_1.31.0.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