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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# mhcnuggetsr
<!-- badges: start -->
[](https://www.tidyverse.org/lifecycle/#stable)
[](https://CRAN.R-project.org/package=mhcnuggetsr)
[]( https://CRAN.R-project.org/package=mhcnuggetsr)
[](https://CRAN.R-project.org/package=mhcnuggetsr)
Branch |[](https://github.com/richelbilderbeek/mhcnuggetsr/actions) | [](https://www.codecov.io)
---------|--------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
`master `| | [](https://codecov.io/github/richelbilderbeek/mhcnuggetsr/branch/master)
`develop`|| [](https://codecov.io/github/richelbilderbeek/mhcnuggetsr/branch/develop)
<!-- badges: end -->
> mhcnuggetsr is broken, see [here](https://github.com/richelbilderbeek/mhcnuggetsr/issues/13),
> as the import of the `MHCnuggets` Python package by `reticulate``
> fails. If you know how to fix this, please contact me
R package to work with [MHCnuggets](https://github.com/KarchinLab/mhcnuggets).
The goal of `mhcnuggetsr` is to predict the half maximal inhibitory concentration
of peptides for an MHC haplotype.
It does by calling [MHCnuggets](https://github.com/KarchinLab/mhcnuggets).
## Installation
You can install the released version of mhcnuggetsr from [GitHub](https://github.com/) with:
```
remotes::install_github("richelbilderbeek/mhcnuggetsr")
```
Install MHCnuggets using the non-CRAN extension
[mhcnuggetsrinstall](https://github.com/richelbilderbeek/mhcnuggetsrinstall):
```
# {r install}
library(mhcnuggetsr)
if (!is_mhcnuggets_installed()) {
remotes::install_github("richelbilderbeek/mhcnuggetsrinstall")
mhcnuggetsrinstall::install_mhcnuggets()
mhcnuggetsr_self_test()
}
```
## Example
Here is how to get the IC50 values (in nM) for the peptides in
an example file:
```
# {r example}
library(testthat)
library(mhcnuggetsr)
if (is_mhcnuggets_installed()) {
mhcnuggets_options <- create_mhcnuggets_options(
mhc = "HLA-A02:01"
)
df <- predict_ic50(
peptides = "AIAACAMLLV",
mhcnuggets_options = mhcnuggets_options
)
expect_equal(df$ic50, 5578.77)
}
```
## How can I suppress the output when making a prediction?
One cannot until MHCnuggets allows to do so.
Issue is posted [here](https://github.com/KarchinLab/mhcnuggets/issues/17).
## There is a feature I miss
See [CONTRIBUTING](CONTRIBUTING.md), at `Submitting use cases`
## I want to collaborate
See [CONTRIBUTING](CONTRIBUTING.md), at 'Submitting code'
## I think I have found a bug
See [CONTRIBUTING](CONTRIBUTING.md), at 'Submitting bugs'
## There's something else I want to say
Sure, just add an Issue. Or send an email.
## External links
* [MHCnuggets GitHub repo](https://github.com/KarchinLab/mhcnuggets)
## References
Article about MHCnuggets:
* Shao, Xiaoshan M., et al. "High-throughput prediction of MHC class I and II
neoantigens with MHCnuggets." Cancer Immunology Research 8.3 (2020): 396-408.