User:Lindenb/Notebook/UMR915/2012/02/27

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Installing ReadDepth: http://code.google.com/p/readdepth/wiki/Documentation

mkdir lib
> install.packages(c("foreach"),"lib")
(...)
> install.packages(c("methods"),"lib")
(...)
> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> biocLite(c("doMC","IRanges","DNAcopy"),lib="lib")
Using R version 2.11.0, biocinstall version 2.6.10.
Installing Bioconductor version 2.6 packages:
[1] "doMC"    "IRanges" "DNAcopy"
(...)
$ R CMD INSTALL -l lib readDepth.tgz

Install Annotations:

$ R

> library("iterators",lib="lib")
(...)
> library("multicore",lib="lib")
> library("doMC",lib="lib")
(...)
> library("readDepth",lib="lib")

> getAnnotations(50,"male", genome="hg19")