systemPipeR (version 1.6.2)

symLink2bam: Symbolic links for IGV

Description

Function for creating symbolic links to view BAM files in a genome browser such as IGV.

Usage

symLink2bam(sysargs, command="ln -s", htmldir, ext = c(".bam", ".bai"), urlbase, urlfile)

Arguments

sysargs

Object of class SYSargs

command

Shell command, defaults to "ln -s"

htmldir

Path to HTML directory with http access.

ext

File name extensions to use for BAM and index files.

urlbase

The base URL structure to use in URL file.

urlfile

Name and path of URL file.

Value

• symbolic links and url file

Examples

## Construct SYSargs object from param and targets files 
param <- system.file("extdata", "tophat.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)

## Create sym links and URL file for IGV
symLink2bam(sysargs=args, command="ln -s", htmldir=c("~/.html/", "somedir/"), ext=c(".bam", ".bai"), urlbase="http://myserver.edu/~username/", urlfile="IGVurl.txt")