README.md

In tavareshugo/MagicHelpR: QTL mapping in Arabidopsis MAGIC lines

:warning: I would strongly advise against using this package! Instead, you can use the R/qtl2 for analysis of MAGIC data. For Arabidopsis specifically, I've written a data package (atMAGIC), which provides a cross2 object to use with that package. Alternatively there's also data available from the R/qtl2data repository.

MagicHelpR

This package was written mostly for personal convenience to help in performing QTL mapping in the Arabidopsis multiparent advanced generation intercross (MAGIC) lines (described in Kover P .. Mott R 2009).

This might however be useful for anyone using the Arabidopsis MAGIC lines. It depends on the happy.hbrem package, which can be installed from https://github.com/tavareshugo/happy.hbrem

The package implements the same linear model approach in the available scripts, but with some more flexibility for specifying models and outputs tabular data that is convenient for downstream analysis and plotting.

To install this package, launch R and issue the following commands:

if(!require("remotes")) install.packages("remotes")
if(!require("happy.hbrem")) remotes::install_github("tavareshugo/happy.hbrem")

remotes::install_github("tavareshugo/MagicHelpR")

# If the above fails (it has done for me in Ubuntu), then do this instead
remotes::install_git("git://github.com/tavareshugo/MagicHelpR.git")

There's also a basic introduction vignette.

tavareshugo/MagicHelpR documentation built on May 4, 2020, 3:01 p.m.