===================== INSTRUCTIONS ==============================

This document contains instructions for installing and using rvHPDT
package for R.


1. Install

For Linux users, download the MERLIN for haplotyping in pedigrees.

For Linux users, download the compiled R package file for Linux:
rvHPDT_1.0.tar.gz
For Windows users, download the compiled R package file for Windows:
rvHPDT_1.0.zip
Then use the following function in R to install the package
>install.packages(pkgs=filename,repos=NULL)
where "filename" should be replaced with the corresponding file name.

Moreover, install the following packages, 
>install.packages(pkgs="gregmisc") 


Moreover, please install MERLIN software that could be downloaded from http://www.sph.umich.edu/csg/abecasis/merlin/tour/haplotyping.html.

2. Use

Use
>library(rvHPDT) 
>library(gtools) 
to load the packages into R.

Use
>?rhapPDT 
to read the instruction.


3. Example 

Using the example data file: MLIP.ped 
 
 
 
ped<-read.table("example.ped",head=1,stringsAsFactors=FALSE)
map<-read.table("example.map",head=1,stringsAsFactors=FALSE)  
test<-rhapPDT(ped, map, trace=TRUE, nperm=10) 
test 
  
  
#     maxH      hPDT    hPDT-t      maxV      vPDT    vPDT-t 
# 0.1818182 0.5910696 0.6061041 0.7272727 0.6483508 0.4081867 


4. Reference 


Guo W , Shugart YY, The power comparison of the haplotype-based collapsing tests and the variant-based collapsing tests for detecting rare variants in pedigrees (manuscript). 

   
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If you have any questions, please email Wei Guo at:
wei.guo3@nih.gov