scoreInvHap
This is the released version of scoreInvHap; for the devel version, see scoreInvHap.
Get inversion status in predefined regions
Bioconductor version: Release (3.23)
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("scoreInvHap")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.34.0 |
| 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 |
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_1.34.0.tar.gz |
| Windows Binary (x86_64) | scoreInvHap_1.34.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | scoreInvHap_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | scoreInvHap_1.34.0.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 |