SpinpharmaR
From INPHARMA wiki
Jump to navigationJump to searchspinpharmaR is an R package which provides functionality to parse and analyse output from spINPHARMA.
Download spinpharmaR from URL: http://www.inpharma-wiki.carlomagno-group.org/downloads/spinpharmar/spinpharmar.tar.gz
To install spinpharmaR (from a Linux terminal):
R CMD INSTALL spinpharmar.tar.gz
Load package:
## Open R
R
## Load spinpharmaR
library(spinpharmaR)
## List functions of the package
ls("package:spinpharmaR")
[1] "calc.rmsd" "filter.hits" "join.rmsd" "plot.noes" "plot.qual"
[6] "print.hits" "print.noes" "print.qual" "read.noes" "read.qual"
For documentation use (in interactive mode):
?function
i.e.:
R
?read.qual
?filter.hits
?plot.qual
See also Analyzing the results for more information on usage.
Dependencies
The RMSD calculation in spinpharmaR depends on the Bio3D (http://thegrantlab.org/bio3d) R-package:
R: http://www.r-project.org Bio3d: http://thegrantlab.org/bio3d
Installation in Ubuntu
To install R, Bio3D, and spinpharmaR:
## Install R
sudo apt-get install r-base
## Install Bio3D
wget http://thegrantlab.org/bio3d/phocadownload/Bio3D_version2.x/bio3d_2.0-1.tar.gz
R CMD INSTALL bio3d_2.0-1.tar.gz
## Install spinpharmaR
wget http://www.carlomagno.embl.de/downloads/spinpharmar/spinpharmar.tar.gz
R CMD INSTALL spinpharmar.tar.gz
Voila !