poim2motif

Assessing motifs in Positional Oligomer Importance Matrices (POIMs).

required installations

1. shogun toolbox
   http://www.shogun-toolbox.org/doc/en/3.0.0/installation.html
   install with python interface
2. openopt
   http://openopt.org/Install
3. R https://cran.r-project.org/mirrors.html
   install the additional package bioconductor package by enter in R
   source("http://bioconductor.org/biocLite.R")
   biocLite("seqLogo")
   

tutorial

"run_toy.py" is the toy Example "run_real1.py" is the real Example. For this real experiment you need to download one folder of the real data from: http://www.fml.tuebingen.mpg.de/raetsch/projects/lsmkl and adjust the datapath in "run_real1.py"

1. create POIM
   by set CURRENT_TASK to TASK_1

2. compute Motif
   by set CURRENT_TASK to TASK_2

With "path" you specify the folder path, including all results. You can choose the Name of the Experiment by experiment_name, which will be the name of the folder including all results.

If you have any questions, please write me a mail at marina.vidovic@tu-berlin.de.

Good luck!