scoreInvHap
This is the development version of scoreInvHap; for the stable release version, see scoreInvHap.
Get inversion status in predefined regions
Bioconductor version: Development (3.20)
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 Pelegrà [aut], Juan R. Gonzalez [aut, cre]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>
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 | ||
LICENSE | Text |
Details
biocViews | Genetics, GenomicVariation, SNP, Software |
Version | 1.27.0 |
In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
License | file LICENSE |
Depends | R (>= 3.6.0) |
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_1.27.0.tar.gz |
Windows Binary | scoreInvHap_1.27.0.zip |
macOS Binary (x86_64) | scoreInvHap_1.27.0.tgz |
macOS Binary (arm64) | scoreInvHap_1.27.0.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 |