scoreInvHap

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6

Get inversion status in predefined regions

Bioconductor version: Development (3.24)

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")):

Carlos Ruiz, Dolors Pelegrí, Juan R. Gonzalez. scoreInvHap: Get inversion status in predefined regions. doi:10.18129/B9.bioc.scoreInvHap, R package version 1.35.0, https://bioconductor.org/packages/scoreInvHap.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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	1.35.0
In Bioconductor since	BioC 3.6 (R-3.4) (9 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, r-universe

Package Archives

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

Source Package	scoreInvHap_1.35.0.tar.gz
Windows Binary (x86_64)	scoreInvHap_1.35.0.zip
macOS Binary (big-sur-x86_64)	scoreInvHap_1.35.0.tgz
macOS Binary (sonoma-arm64)	scoreInvHap_1.35.0.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