From 5ac175dfa7df6d860d887424879b2a5a1583e07b Mon Sep 17 00:00:00 2001 From: Joe Zhu Date: Fri, 14 Oct 2016 17:15:08 +0100 Subject: [PATCH] update submodule, and README --- .DEploid | 2 +- README.md | 51 ++++++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 51 insertions(+), 2 deletions(-) diff --git a/.DEploid b/.DEploid index c2f3236..0255a63 160000 --- a/.DEploid +++ b/.DEploid @@ -1 +1 @@ -Subproject commit c2f3236c53713def2681db07c43b3db3d248d914 +Subproject commit 0255a63973ce2ccb1fb5289ec9dfecebe6e6344f diff --git a/README.md b/README.md index b248dd7..89a3ca6 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,55 @@ [![Build Status](https://travis-ci.org/mcveanlab/DEploid-r.svg?branch=master)](https://travis-ci.org/mcveanlab/DEploid-r) [![Build Status](https://ci.appveyor.com/api/projects/status/hi1nq97d5l68qs4r?svg=true)](https://ci.appveyor.com/project/shajoezhu/deploid-r) - +DEploid R package +================= `dEploid` is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting. + + +Installation +------------ + +Please install `Rcpp` package first. From the `R`-console, type +```R +install.packages("Rcpp") +``` + +On specific operating systems, please carry out the following: + +### Unix-like system + +```R +install.packages("DEploid_0.3.1.tar.gz", repos=NULL) +``` + +### Windows + +Please first install [https://cran.r-project.org/bin/windows/Rtools/](`Rtools`), then +```R +install.packages("DEploid_0.3.1.tar.gz", repos=NULL) +``` + +Usage +----- + +Please refer to the help page and examples for each function. For example, +```R +library(DEploid) +?dEploid +?plotProportions +``` + +Licence +------- + +You can freely use all code in this project under the conditions of the GNU GPL Version 3 or later. + + +Citation +-------- + +If you use `dEploid` in your work, please cite the program: + +PLACEHOLDER FOR APP NOTE +