README.md

In geo047/HapSampler: QTL-marker haplotype builder

HapSampler

An R package for building joint marker and qtl haplotypes via Markov chain Monte Carlo methods. The package requires phenotypic and haplotype data. The phenotypic data must contain a trait (either continuous or binary), and an animal id. The haplotype data are the maternal and paternal haplotypes. These haploytpes can be obtained from unphased genotype data via phasing programs such as BEAGLE and fastPAHSE.

Once the package has been installed (see below), a listing of its functions can be obtained from within your R session via the command:

library(, HapSampler)

and documentation on the running of any command can be seen with the help command. For example, to obtain help on the hapsampler command, use

help(hapsampler)

Installation

This package is best installed from within R.

To install the package, directly from github, you need the "devtools" package which can be installed with

install.packages("devtools")

Then, to install the HapSampler package, run the commands

library("devtools")
devtools::install_github("geo047/HapSampler")

Suppose, you would like to install "HapSampler" into a local directory, say /home/id/RLib

Then, you just need to add a ".libPaths" command as follows

library("devtools")
.libPaths(c(.libPaths(), "/home/id/RLib"))
devtools::install_github("geo047/HapSampler")

geo047/HapSampler documentation built on May 17, 2019, 1:11 a.m.