haploview {genomic}R Documentation

Call the haploview program on data

Description

Calls the haploview java program.

Usage

haploview(a,externalprog="haploview")

Arguments

a A list of type mutatedARG or any other list that contains values ss, var, a vector of positions pos and matrix of genetic value d
externalprog

{The name (and optionally path) to a shell script that runs the haploview program. }

Value

0 if successful.

Note

You need a working version of haploview that is in the path (or alternatively provide the full path in externalprog).

The haploview file should look something like:

#!/bin/sh

/usr/local/j2sdk1.4.2_07/bin/java -jar /data/programs/haploview/Haploview.jar $@

Author(s)

Ian J. Wilson <I.J.Wilson@ncl.ac.uk>

References

http://www.broad.mit.edu/mpg/haploview/index.php

Examples

data(sim1)
haploview(sim1)

library(ARG)
g <- mutate(simARG(100,1000,0.01),100,"panel(2)")
haploview(g)

[Package genomic version 1.0 Index]