This repository contains the code for the BIITE algorithm, which infers peptide:HLA immunogenicity from ELISpot data.

To install, you can use devtools

#if you don't have devtools, install it

Example data is available in Data; an example script is available in Example/example.r. This example script uses the example data. Before you run the example script, make sure to use


to make sure the output goes where you want it to go.

To run it with your own data, you can adapt the example script; I've tried to indicate what should be (un)commented and changed by the user. Input data should at least contain: - for each HLA: a column with the copy number per patient - for each peptide: a Boolean column indicating whether the ELISpot for this peptide came up positive (TRUE) or negative, for each patient.

A small example of input data:

|Patient| DQB1_02 |DQB1_03 |DQB1_04 |DQB1_05 |DQB1_06 |pep_1 |pep_2 |pep_3| |-------|---------|---------|---------|---------|---------|-------|-------|-----| |Pat_1 |1 |0 |0 |0 |1 |TRUE |TRUE |TRUE| |Pat_2 |1 |1 |0 |0 |0 |TRUE |TRUE |TRUE| |Pat_3 |0 |2 |0 |0 |0 |TRUE |FALSE |FALSE| |Pat_4 |0 |0 |0 |2 |0 |TRUE |TRUE |TRUE| |Pat_5 |0 |0 |2 |0 |0 |TRUE |TRUE |FALSE| |Pat_6 |1 |0 |0 |0 |1 |FALSE |FALSE |TRUE|

We have submitted the BIITE paper for publication in a peer-reviewed journal. Please email me ([email protected]) for a reference (I will add one as soon as the paper has been accepted).

I'm happy to provide support, just drop me a line!

liesb/BIITE documentation built on May 21, 2017, 1:35 p.m.