===================== 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") 



2. Use

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

Use
>?rhapPDT 
to read the instruction.


3. Example 

Using the example data file: MLIP.ped 
 
 
 
ped<-read.table("MLIP.ped",head=1,stringsAsFactors=FALSE)
map<-read.table("CFS.merlin.map",head=1,stringsAsFactors=FALSE)  
test<-rhapPDT(ped, map, trace=TRUE) 
test 

#$hPDT_v0
#[1] 0.4231359

#$hPDT_v1
#[1] 0.1481145

#$rvPDT_v0
#[1] 0.03237073

#$rvPDT_v1
#[1] 0.162997
 
 
 

4. Reference 


Guo W , Shugart YY, Does Haplotype-based Collapsing Tests Gain More Power than 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