netmhc2pan
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R package for NetMHCIIpan [1].
Please note that this page is intended for academic users only. Other users are requested to contact the Software Package Manager at [email protected]
Install
Use usethis
(or devtools
) to install the netmhc2pan
package:
usethis::install_github("richelbilderbeek/netmhc2pan")
Load the netmhc2pan
library:
library(netmhc2pan)
Install NetMHCIIpan to a default folder using netmhc2pan
and a download URL.
The download URL can be obtained from the
NetMHCIIpan website at
https://services.healthtech.dtu.dk/service.php?NetMHCIIpan-3.2
and expires after four hours.
install_netmhc2pan("https://services.healthtech.dtu.dk/download/fb4dee93-ddbb-4639-ab21-45fdfd0ed23e")
Installation troubleshooting
URL is expired
Request a new download link
cannot open URL 'https://services.healthtech.dtu.dk/download/[number]/netMHCIIpan-3.2.Linux.tar.gz'
From a fresh download link, you can download the file,
yet not install using the install_netmhc2pan
function.
In that case, use the install_netmhc2pan_bin_from_file
function:
install_netmhc2pan_bin_from_file("netMHCIIpan-3.2.Linux.tar.gz")
This function assumes that the file netMHCIIpan-3.2.Linux.tar.gz
is in the working
directory.
After this, install like normal:
install_netmhc2pan()
cannot open URL 'https://www.cbs.dtu.dk/services/NetMHCIIpan-3.2/data.Linux.tar.gz'
This happens when the university website is down (yes, this has happened!).
In that case, use the install_netmhc2pan_data_from_file
function:
install_netmhc2pan_data_from_file("data.Linux.tar.gz")
This function assumes that the file data.Linux.tar.gz
is in the working
directory.
After this, install like normal:
install_netmhc2pan()
Usage
We start from a FASTA file with one or more protein sequences:
fasta_filename <- system.file(
"extdata", "example.fasta", package = "netmhc2pan"
)
This is how to content of such a FASTA file looks like:
message(readLines(fasta_filename), sep = "\n")
>sp|L0T550|RIP2_MYCTU_158_180
AVLWAGVAFLAFLQLTALVLNLL
MHC2 has multiple alleles that bind differently to protein parts. NetMHCIIpan supports more than 5000 alleles:
all_alleles <- get_netmhc2pan_alleles()
testit::assert(length(all_alleles) > 5000)
We simply pick the first two alleles:
alleles <- all_alleles[1:2]
Running the NetMHCIIpan analysis:
bindings <- run_netmhc2pan(
fasta_filename = fasta_filename,
alleles = alleles
)
The data frame bindings
contains the results:
knitr::kable(bindings)
Pos | Peptide | ID | Allele | one_minus_log50k | nM | Rank |
---|---|---|---|---|---|---|
1 | AVLWAGVAFLAFLQL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0101 | 0.510 | 201.09 | 39.0 |
2 | VLWAGVAFLAFLQLT | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0101 | 0.475 | 293.98 | 47.0 |
3 | LWAGVAFLAFLQLTA | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0101 | 0.524 | 172.31 | 36.0 |
4 | WAGVAFLAFLQLTAL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0101 | 0.566 | 109.07 | 26.0 |
5 | AGVAFLAFLQLTALV | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0101 | 0.602 | 73.94 | 19.0 |
6 | GVAFLAFLQLTALVL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0101 | 0.680 | 31.93 | 7.0 |
7 | VAFLAFLQLTALVLN | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0101 | 0.688 | 29.20 | 6.5 |
8 | AFLAFLQLTALVLNL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0101 | 0.680 | 32.04 | 7.0 |
9 | FLAFLQLTALVLNLL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0101 | 0.669 | 35.92 | 8.5 |
1 | AVLWAGVAFLAFLQL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0102 | 0.346 | 1188.96 | 38.0 |
2 | VLWAGVAFLAFLQLT | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0102 | 0.329 | 1414.85 | 44.0 |
3 | LWAGVAFLAFLQLTA | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0102 | 0.379 | 823.82 | 28.0 |
4 | WAGVAFLAFLQLTAL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0102 | 0.406 | 616.05 | 21.0 |
5 | AGVAFLAFLQLTALV | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0102 | 0.425 | 504.55 | 17.0 |
6 | GVAFLAFLQLTALVL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0102 | 0.458 | 353.10 | 11.0 |
7 | VAFLAFLQLTALVLN | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0102 | 0.456 | 360.90 | 11.0 |
8 | AFLAFLQLTALVLNL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0102 | 0.456 | 361.54 | 11.0 |
9 | FLAFLQLTALVLNLL | sp|L0T550|RIP2_MYCTU_158_180 | DRB1_0102 | 0.442 | 420.88 | 14.0 |
The strongest binding is between the MHC2 allele DRB1_0101
at the 7th (to and including 21st) amino acid of the sp|L0T550|RIP2_MYCTU_158_180
protein, as it is in the top 6.5% of best binders.
FAQ
netmhc2pan
work?
Under which operating systems does netmhc2pan
can only work on the set of operating systems NetMHCIIpan
works on. Currently, only Linux is supported:
Operating system | Supported by NetMHCIIpan | Supported by netmhc2pan |
---|---|---|
Darwin | Y | N |
Linux | Y | Y |
Windows | N | N |
Can't locate Env.pm in @INC
?
How to solve Install the Perl Env
package with:
/usr/bin/perl -MCPAN -e 'install Env'
See notes at this Issue.
Are there similar packages?
These are the ones I use:
- mhcnuggetsr: predicts IC50 values for MHC-I and MHC-II haplotypes
- epitope-prediction: predicts IC50 values for MHC-I haplotypes
References
- [1] Improved methods for predicting peptide binding affinity to MHC class II molecules. Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M. Immunology. 2018 Jan 6. doi: 10.1111/imm.12889. PubMed: 29315598