predict_ic50 {mhcnuggetsr} | R Documentation |
Predict the half maximal inhibitory concentration (aka IC50) (in nM) for one or more peptides. Each peptide must be 15 amino acids at most (use predict_ic50s to predict the IC50s for longer peptides)
predict_ic50(
mhcnuggets_options,
peptides,
peptides_path = create_temp_peptides_path()
)
mhcnuggets_options |
options to run MHCnuggets with, as can be created by create_mhcnuggets_options. |
peptides |
one of more peptide sequences |
peptides_path |
the path to the peptides |
a tibble with two columns:
(1) peptide
, which holds the peptide sequence, and
(2) ic50
, which holds the predicted IC50
this function uses a temporary file, because MHCnuggets reads its input from file. This temporary file is deleted after this function passed successfully.
Richèl J.C. Bilderbeek
if (is_mhcnuggets_installed()) {
peptides <- c("AIAACAMLLV", "ALVCYIVMPV", "ALEPRKEIDV")
mhc_1_haplotype <- "HLA-A02:01"
mhcnuggets_options <- create_mhcnuggets_options(
mhc = mhc_1_haplotype
)
predict_ic50(
peptides = peptides,
mhcnuggets_options = mhcnuggets_options
)
}