scoreInvHap
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see scoreInvHap.
Get inversion status in predefined regions
Bioconductor version: 3.7
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 two well known inversions (8p23 and 17q21.31) and for two additional regions.
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 "3.5") 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")| Call haplotype inversions with scoreInvHap | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Genetics, GenomicVariation, SNP, Software |
| Version | 1.2.1 |
| 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_1.2.1.tar.gz |
| Windows Binary | scoreInvHap_1.2.1.zip |
| Mac OS X 10.11 (El Capitan) | scoreInvHap_1.2.1.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 3.7 | Source Archive |