QTLExperiment

S4 classes for QTL summary statistics and metadata

Bioconductor version: Release (3.20)

QLTExperiment defines an S4 class for storing and manipulating summary statistics from QTL mapping experiments in one or more states. It is based on the 'SummarizedExperiment' class and contains functions for creating, merging, and subsetting objects. 'QTLExperiment' also stores experiment metadata and has checks in place to ensure that transformations apply correctly.

Author: Christina Del Azodi [aut], Davis McCarthy [ctb], Amelia Dunstone [cre, ctb]

Maintainer: Amelia Dunstone <amelia.dunstone at svi.edu.au>

Citation (from within R, enter citation("QTLExperiment")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("QTLExperiment")

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("QTLExperiment")

An introduction to the QTLExperiment class	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, DataRepresentation, FunctionalGenomics, Infrastructure, SNP, Sequencing, Software
Version	1.4.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
License	GPL-3
Depends	SummarizedExperiment
Imports	methods, rlang, checkmate, dplyr, collapse, vroom, tidyr, tibble, utils, stats, ashr, S4Vectors, BiocGenerics
System Requirements
URL	https://github.com/dunstone-a/QTLExperiment
Bug Reports	https://github.com/dunstone-a/QTLExperiment/issues

Suggests	testthat, BiocStyle, knitr, rmarkdown, covr
Linking To
Enhances
Depends On Me	multistateQTL
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	QTLExperiment_1.4.0.tar.gz
Windows Binary (x86_64)	QTLExperiment_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	QTLExperiment_1.4.0.tgz
macOS Binary (arm64)	QTLExperiment_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/QTLExperiment
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/QTLExperiment
Bioc Package Browser	https://code.bioconductor.org/browse/QTLExperiment/
Package Short Url	https://bioconductor.org/packages/QTLExperiment/
Package Downloads Report	Download Stats