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)
}These are the MHC-I haplotypes that have a trained model.
These are the MHC-II haplotypes that have a trained model.
mhcnuggetsr_report()
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