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demo

library(knitr)
library(mhcnuggetsr)
library(testthat)

For this vignette, we use the same example as the MHCnuggets Python notebooks.

Get the path to the testing peptides, and show them:

if (is_mhcnuggets_installed()) {
  peptides_path <- get_example_filename("test_peptides.peps")
  expect_true(file.exists(peptides_path))
  readLines(peptides_path, warn = FALSE)
}

Pick an MHC-I haplotype:

if (is_mhcnuggets_installed()) {
  mhc_1_haplotype <- "HLA-A02:01"
  expect_true(mhc_1_haplotype %in% get_trained_mhc_1_haplotypes())
}

Predict:

#{r mhc1_predict_ic50_from_file_no_ba_models}
if (is_mhcnuggets_installed()) {
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_1_haplotype
  )
  df <- predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
  kable(df)
}

Predict:

#{r mhc1_predict_ic50_from_file_ba_models}
if (is_mhcnuggets_installed()) {
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_1_haplotype,
    ba_models = TRUE
  )
  df <- predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
  kable(df)
}

Use MCH-II haplotype:

if (is_mhcnuggets_installed()) {
  mhc_2_haplotype <- "HLA-DRB101:01"
  expect_true(mhc_2_haplotype %in% get_trained_mhc_2_haplotypes())
}

Predict:

#{r mhc2_predict_ic50_from_file_no_ba_models}
if (is_mhcnuggets_installed()) {
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_2_haplotype
  )
  df <- predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
  kable(df)
}

Use another MHC-I haplotype. In this case, MHCnuggets has not been trained upon it, but it is a valid supertype:

if (is_mhcnuggets_installed()) {
  mhc_1_haplotype <- "HLA-A02:60"
  expect_false(mhc_1_haplotype %in% get_trained_mhc_1_haplotypes())
}

Predict:

#{r predict_mhc_1_haplotype_supertype}
if (is_mhcnuggets_installed()) {
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc_class = "I",
    mhc = mhc_1_haplotype
  )
  df <- predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
  kable(df)
}

Appendix

All example files

if (is_mhcnuggets_installed()) {
  basename(get_example_filenames())
}

All MHC-I haplotypes

These are the MHC-I haplotypes that have a trained model.

if (is_mhcnuggets_installed()) {
  cat(get_trained_mhc_1_haplotypes())
}

All MHC-II haplotypes

These are the MHC-II haplotypes that have a trained model.

if (is_mhcnuggets_installed()) {
  cat(get_trained_mhc_2_haplotypes())
}

Session info

mhcnuggetsr_report()
#> ***************
#> * mhcnuggetsr *
#> ***************
#> OS: unix
#> **************
#> * MHCnuggets *
#> **************
#> Is MHCnuggets installed: FALSE
#> ****************
#> * session info *
#> ****************
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.3 (2024-02-29)
#>  os       Ubuntu 24.04.4 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language (EN)
#>  collate  C
#>  ctype    en_US.UTF-8
#>  tz       Europe/Stockholm
#>  date     2026-07-04
#>  pandoc   3.1.3 @ /usr/bin/ (via rmarkdown)
#>  quarto   1.3.450 @ /usr/local/bin/quarto
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  brio          1.1.5   2024-04-24 [2] CRAN (R 4.3.3)
#>  bslib         0.11.0  2026-05-16 [2] CRAN (R 4.3.3)
#>  cachem        1.1.0   2024-05-16 [2] CRAN (R 4.3.3)
#>  cli           3.6.6   2026-04-09 [2] CRAN (R 4.3.3)
#>  devtools      2.5.2   2026-04-30 [2] CRAN (R 4.3.3)
#>  digest        0.6.39  2025-11-19 [2] CRAN (R 4.3.3)
#>  ellipsis      0.3.3   2026-04-04 [2] CRAN (R 4.3.3)
#>  evaluate      1.0.5   2025-08-27 [2] CRAN (R 4.3.3)
#>  fastmap       1.2.0   2024-05-15 [2] CRAN (R 4.3.3)
#>  fs            2.1.0   2026-04-18 [2] CRAN (R 4.3.3)
#>  glue          1.8.1   2026-04-17 [2] CRAN (R 4.3.3)
#>  htmltools     0.5.9   2025-12-04 [2] CRAN (R 4.3.3)
#>  jquerylib     0.1.4   2021-04-26 [2] CRAN (R 4.3.3)
#>  jsonlite      2.0.0   2025-03-27 [2] CRAN (R 4.3.3)
#>  knitr       * 1.51    2025-12-20 [2] CRAN (R 4.3.3)
#>  lifecycle     1.0.5   2026-01-08 [2] CRAN (R 4.3.3)
#>  magrittr      2.0.5   2026-04-04 [2] CRAN (R 4.3.3)
#>  memoise       2.0.1   2021-11-26 [2] CRAN (R 4.3.3)
#>  mhcnuggetsr * 1.2.6   2026-07-04 [1] local
#>  otel          0.2.0   2025-08-29 [2] CRAN (R 4.3.3)
#>  pkgbuild      1.4.8   2025-05-26 [2] CRAN (R 4.3.3)
#>  pkgload       1.5.2   2026-04-22 [2] CRAN (R 4.3.3)
#>  purrr         1.2.2   2026-04-10 [2] CRAN (R 4.3.3)
#>  R6            2.6.1   2025-02-15 [2] CRAN (R 4.3.3)
#>  rappdirs      0.3.4   2026-01-17 [2] CRAN (R 4.3.3)
#>  rlang         1.2.0   2026-04-06 [2] CRAN (R 4.3.3)
#>  rmarkdown     2.31    2026-03-26 [2] CRAN (R 4.3.3)
#>  sass          0.4.10  2025-04-11 [2] CRAN (R 4.3.3)
#>  sessioninfo   1.2.3   2025-02-05 [2] CRAN (R 4.3.3)
#>  testthat    * 3.3.2   2026-01-11 [2] CRAN (R 4.3.3)
#>  usethis       3.2.1   2025-09-06 [2] CRAN (R 4.3.3)
#>  vctrs         0.7.3   2026-04-11 [2] CRAN (R 4.3.3)
#>  xfun          0.57    2026-03-20 [2] CRAN (R 4.3.3)
#>  yaml          2.3.12  2025-12-10 [2] CRAN (R 4.3.3)
#> 
#>  [1] /tmp/RtmpjAub9Z/Rinsta2095ae47f80
#>  [2] /home/richel/R/x86_64-pc-linux-gnu-library/4.3
#>  [3] /usr/local/lib/R/site-library
#>  [4] /usr/lib/R/site-library
#>  [5] /usr/lib/R/library
#>  * ── Packages attached to the search path.
#> 
#> ──────────────────────────────────────────────────────────────────────────────

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