qtl2-package: qtl2: Quantitative Trait Locus Mapping in Experimental...

In rqtl/qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Description

Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1534/genetics.118.301595")}.

Vignettes

• user guide

• categorized list of functions in R/qtl2

• input file formats

• using qtl2fst for on-disk genotype probabilities

• preparing DO mouse data for R/qtl2

• genotype diagnostics for diversity outbred mice

• identifying sample mix-ups in diversity outbred mice

• differences between R/qtl and R/qtl2

• developer guide

• Tutorial on R/qtl2 by Susan McClatchy and Dan Gatti

Related packages

• qtl2convert, for converting data among the R/qtl2, DOQTL, and R/qtl formats

• qtl2fst, for storing genotype probabilities on disk

• qtl2ggplot, for ggplot2-based data visualizations

Author(s)

Maintainer: Karl W Broman [e-mail] (ORCID)

Other contributors:

• R Core Team [contributor]

See Also

Useful links:

• https://kbroman.org/qtl2/

• https://github.com/rqtl/qtl2

• Report bugs at https://github.com/rqtl/qtl2/issues

rqtl/qtl2 documentation built on March 20, 2024, 6:35 p.m.