scoreInvHap
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see scoreInvHap.
Get inversion status in predefined regions
Bioconductor version: 3.11
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, cre], Juan R. Gonzalez [aut]
Maintainer: Carlos Ruiz <carlos.ruiz at isglobal.org>
citation("scoreInvHap")):
Installation
To install this package, start R (version "4.0") 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 | ||
| LICENSE | Text |
Details
| biocViews | Genetics, GenomicVariation, SNP, Software |
| Version | 1.10.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | testthat, knitr, BiocStyle, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scoreInvHap_1.10.0.tar.gz |
| Windows Binary | scoreInvHap_1.10.0.zip |
| macOS 10.13 (High Sierra) | scoreInvHap_1.10.0.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 3.11 | Source Archive |