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scoreInvHap

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

Get inversion status in predefined regions


Bioconductor version: Development (3.19)

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 "4.4") 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

Details

biocViews Genetics, GenomicVariation, SNP, Software
Version 1.25.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License file LICENSE
Depends R (>= 3.6.0)
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_1.25.0.tar.gz
Windows Binary scoreInvHap_1.25.0.zip (64-bit only)
macOS Binary (x86_64) scoreInvHap_1.25.0.tgz
macOS Binary (arm64) scoreInvHap_1.25.0.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/
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