README.md

BIITE

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
install.packages("devtools")
library(devtools)
devtools::install_github("liesb/BIITE")

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

setwd("some/directory")

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.