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 (lies.boelen@gmail.com) 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!