Title:	Call MHCnuggets
Version:	1.1
Maintainer:	Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>
Description:	MHCnuggets (https://github.com/KarchinLab/mhcnuggets) is a Python tool to predict MHC class I and MHC class II epitopes. This package allows one to call MHCnuggets from R.
License:	GPL-3
Imports:	rappdirs, reticulate, stringr, tibble
Suggests:	knitr, testthat, rmarkdown
Encoding:	UTF-8
LazyData:	true
RoxygenNote:	7.1.1
URL:	https://github.com/richelbilderbeek/mhcnuggetsr/
BugReports:	https://github.com/richelbilderbeek/mhcnuggetsr
Language:	en-US
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2020-10-27 09:13:47 UTC; richel
Author:	Richèl J.C. Bilderbeek [aut, cre]
Repository:	CRAN
Date/Publication:	2020-11-04 11:30:02 UTC

Are these MHCnuggets names?

Description

Determine if an HLA haplotype name follow the name format that MHCnuggets uses internally

Usage

are_mhcnuggets_names(mhcs)

Arguments

Value

a vector of booleans, TRUE for HLA haplotypes that follow the MHCnuggets naming convention

Examples

if (is_mhcnuggets_installed()) {
  are_mhcnuggets_names(get_mhc_1_haplotypes())
  are_mhcnuggets_names(get_mhc_2_haplotypes())
}

Check the MHC class.

Description

Check the MHC class. Will stop if it is invalid.

Usage

check_mhc_class(mhc_class)

Arguments

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Examples

check_mhc_class("I")
check_mhc_class("II")
check_mhc_class(NA)

Check if MHCnuggets is installed.

Description

Check if MHCnuggets is installed. Will stop if not.

Usage

check_mhcnuggets_installation(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Details

An MHCnuggets installation has two parts:

1. The installation of the Python package, for running the code

2. The download of the Python source code, which allows the use of example files

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  check_mhcnuggets_installation()
}

Check the MHCnuggets options.

Description

Check the MHCnuggets options. Will stop if the options are invalid.

Usage

check_mhcnuggets_options(mhcnuggets_options)

Arguments

Note

an mhcnuggets_options created by create_mhcnuggets_options is always checked by check_mhcnuggets_options

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  check_mhcnuggets_options(create_test_mhcnuggets_options())
}

Check the names of the elements in an mhcnuggets_options list.

Description

Check the names of the elements in an mhcnuggets_options list. Will stop if an element is missing.

Usage

check_mhcnuggets_options_names(mhcnuggets_options)

Arguments

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  check_mhcnuggets_options_names(
    create_test_mhcnuggets_options()
  )
}

Create a set of MHCnuggets options.

Description

Create a set of options to run MHCnuggets with.

Usage

create_mhcnuggets_options(
  mhc_class = NA,
  mhc,
  ba_models = FALSE,
  verbose = FALSE,
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Details

This function will give an error message if the arguments are invalid.

Value

an mhcnuggets_options

Note

an mhcnuggets_options created by create_mhcnuggets_options is always checked by check_mhcnuggets_options

Author(s)

Richèl J.C. Bilderbeek

See Also

use create_test_mhcnuggets_options to create an MHCnuggets object for testing

Examples

if (is_mhcnuggets_installed()) {
  create_mhcnuggets_options(
    mhc = "HLA-A02:01"
  )
}

Create a path to a non-existing temporary file

Description

Create a path to a non-existing temporary file

Usage

create_temp_peptides_path(fileext = ".fasta")

Arguments

Author(s)

Richèl J.C. Bilderbeek

Examples

create_temp_peptides_path()

Create testing options for MHCnuggets

Description

Create a set of testing options to run MHCnuggets with. The most important setting is the use of a specific haplotype.

Usage

create_test_mhcnuggets_options(
  mhc_class = NA,
  mhc = "HLA-A02:01",
  ba_models = FALSE,
  verbose = FALSE,
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  create_test_mhcnuggets_options()
}

This function does nothing. It is intended to inherit the documentation of the parameters from.

Description

This function does nothing. It is intended to inherit the documentation of the parameters from.

Usage

default_params_doc(
  ba_models,
  folder_name,
  mhc,
  mhcs,
  mhc_class,
  mhcnuggets_options,
  mhcnuggets_url,
  n_aas,
  peptide,
  peptides,
  peptide_length,
  peptides_path,
  protein_sequence,
  verbose
)

Arguments

Note

This is an internal function, so it should be marked with @noRd. This is not done, as this will disallow all functions to find the documentation parameters

Author(s)

Richèl J.C. Bilderbeek

Downgrade pip.

Description

Set the version of pip to a specific earlier version.

Usage

downgrade_pip(version = "9.0.0")

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

use upgrade_pip to set pip to the latest version. Use set_pip_version to install a specific version of pip

Examples

## Not run: 
  if (is_pip_installed()) {
    downgrade_pip()
  }

## End(Not run)

Get the path to the folder where this package installs MHCnuggets by default

Description

Get the path to the folder where this package installs MHCnuggets by default

Usage

get_default_mhcnuggets_folder()

Value

the path to the folder where this package installs MHCnuggets by default

Author(s)

Richèl J.C. Bilderbeek

Examples

get_default_mhcnuggets_folder()

Get the full path to an MHCnuggets example file

Description

Get the full path to an MHCnuggets example file

Usage

get_example_filename(
  filename = "test_peptides.peps",
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

the full path to an MHCnuggets example file

Author(s)

Richèl J.C. Bilderbeek

See Also

use get_example_filenames to get all MHCnuggets example filenames

Examples

if (is_mhcnuggets_installed()) {
  get_example_filename("test_peptides.peps")
}

Get the full path to all MHCnuggets example files

Description

Get the full path to all MHCnuggets example files

Usage

get_example_filenames(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

a character vector with all MHCnuggets example files

Author(s)

Richèl J.C. Bilderbeek

See Also

use get_example_filename to get the full path to a MHCnuggets example file

Examples

if (is_mhcnuggets_installed()) {
  get_example_filenames()
}

Get all the MHC-I haplotypes

Description

Get all the MHC-I haplotypes that MHCnuggets has been trained upon.

Usage

get_mhc_1_haplotypes(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

a character vector with haplotype names in MHCnuggets format

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  get_mhc_1_haplotypes()
}

Get all the MHC-II haplotypes

Description

Get all the MHC-II haplotypes that MHCnuggets has been trained upon.

Usage

get_mhc_2_haplotypes(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

a character vector with haplotype names in MHCnuggets format

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  get_mhc_2_haplotypes()
}

Get the URL of the MHCnuggets source code

Description

Get the URL of the MHCnuggets source code

Usage

get_mhcnuggets_url()

Value

a string that is a URL

Author(s)

Richèl J.C. Bilderbeek

Examples

get_mhcnuggets_url()

Get the MHCnuggets version

Description

Get the MHCnuggets version

Usage

get_mhcnuggets_version(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

a string that is a version, for example 2.3.2

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  get_mhcnuggets_version()
}

Get the version of pip

Description

Get the version of pip

Usage

get_pip_version()

Value

a string that is a version, for example 20.2

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pip_installed()) {
  get_pip_version()
}

Get the version of all Python packages

Description

Get the version of all Python packages

Usage

get_python_package_versions()

Value

a tibble with two columns: (1) package, the name of the package, for example absl-py, (2) version, the version of that package, for example 0.9.0

Author(s)

Richèl J.C. Bilderbeek

Examples

if (rappdirs::app_dir()$os != "win" && is_pip_installed()) {
  get_python_package_versions()
}

Get all the MHC-I haplotypes that have been trained on a model

Description

Get all the MHC-I haplotypes that have been trained on a model

Usage

get_trained_mhc_1_haplotypes(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

a character vector with haplotype names in MHCnuggets format

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  get_trained_mhc_1_haplotypes()
}

Get all the MHC-II haplotypes that have been trained on a model

Description

Get all the MHC-II haplotypes that have been trained on a model

Usage

get_trained_mhc_2_haplotypes(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

a character vector with haplotype names in MHCnuggets format

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  get_trained_mhc_2_haplotypes()
}

Install the MHCnuggets Python package.

Description

Install the MHCnuggets Python package.

Usage

install_mhcnuggets(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Examples

## Not run: 
  install_mhcnuggets()

## End(Not run)

Install pip.

Description

Install pip.

Usage

install_pip()

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Examples

## Not run: 
  install_pip()

## End(Not run)

Check if MHCnuggets is installed

Description

Check if MHCnuggets is installed

Usage

is_mhcnuggets_installed(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

TRUE if MHCnuggets is installed

Author(s)

Richèl J.C. Bilderbeek

Examples

is_mhcnuggets_installed()

Is this an MHCnuggets name?

Description

Determine if an HLA haplotype name follow the name format that MHCnuggets uses internally

Usage

is_mhcnuggets_name(mhc)

Arguments

Value

TRUE if the name follows the MHCnuggets naming convention

Examples

# The official name is not the name format used by MHCnuggets
is_mhcnuggets_name("HLA-A*01:01")

# MHCnuggets uses names without the asterisk
is_mhcnuggets_name("HLA-A01:01")

Is this a mhcnuggets_options?

Description

Determine if the MHCnuggets options is valid.

Usage

is_mhcnuggets_options(mhcnuggets_options)

Arguments

Value

TRUE if this a valid set of MHCnuggets options

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  is_mhcnuggets_options(create_test_mhcnuggets_options())
}

Determines if the environment is AppVeyor

Description

Determines if the environment is AppVeyor

Usage

is_on_appveyor()

Value

TRUE if run on AppVeyor, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Examples

is_on_appveyor()

Determines if the environment is a continuous integration service

Description

Determines if the environment is a continuous integration service

Usage

is_on_ci()

Value

TRUE if run on AppVeyor or Travis CI, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Examples

is_on_ci()

Determines if the environment is Travis CI

Description

Determines if the environment is Travis CI

Usage

is_on_travis()

Value

TRUE if run on Travis CI, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Examples

is_on_travis()

Determine if pip is installed

Description

Determine if pip is installed

Usage

is_pip_installed()

Value

TRUE if pip is installed, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Examples

is_pip_installed()

mhcnuggetsr: estimate the topoplogy of membrane proteins

Description

Proteins reside in either the cell plasma of in the cell membrane. A membrane protein goes through the membrane at least once. There are multiple ways to span this hydrophobic layer. One common structure is the transmembrane (alpha) helix (TMH). Given the amino acid sequence of a membrane protein, this package predicts which parts of the protein are TMHs

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {

  peptides_path <- get_example_filename("test_peptides.peps")
  mhc_1_haplotype <- "HLA-A02:01"

  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_1_haplotype
  )

  predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
}

Create a mhcnuggetsr report, to be used when reporting bugs

Description

Create a mhcnuggetsr report, to be used when reporting bugs

Usage

mhcnuggetsr_report(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Author(s)

Richèl J.C. Bilderbeek

Examples

## Not run: 
  mhcnuggetsr_report()

## End(Not run)

Self-test the package

Description

Self-test the package

Usage

mhcnuggetsr_self_test(mhcnuggets_options = create_test_mhcnuggets_options())

Arguments

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {
  mhcnuggetsr_self_test()
}

Predict the IC50 for peptides.

Description

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)

Usage

predict_ic50(
  mhcnuggets_options,
  peptides,
  peptides_path = create_temp_peptides_path()
)

Arguments

Value

a tibble with two columns: (1) peptide, which holds the peptide sequence, and (2) ic50, which holds the predicted IC50

Note

this function uses a temporary file, because MHCnuggets reads its input from file. This temporary file is deleted after this function passed successfully.

Author(s)

Richèl J.C. Bilderbeek

Examples

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
  )
}

Predict the half maximal inhibitory concentration (aka IC50) (in nM) for one or more peptides as saved in a file. Each peptide must be 15 amino acids at most (use predict_ic50s to predict the IC50s for longer peptides)

Description

Predict the half maximal inhibitory concentration (aka IC50) (in nM) for one or more peptides as saved in a file. Each peptide must be 15 amino acids at most (use predict_ic50s to predict the IC50s for longer peptides)

Usage

predict_ic50_from_file(
  mhcnuggets_options,
  peptides_path,
  mhcnuggets_output_filename = mhcnuggetsr::create_temp_peptides_path(fileext = ".csv")
)

Arguments

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {

  peptides_path <- get_example_filename("test_peptides.peps")
  mhc_1_haplotype <- "HLA-A02:01"
  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = mhc_1_haplotype
  )

  predict_ic50_from_file(
    peptides_path = peptides_path,
    mhcnuggets_options = mhcnuggets_options
  )
}

Predict the half maximal inhibitory concentrations (aka IC50s) (in nM) of all possible n-mers within a peptide

Description

Predict the half maximal inhibitory concentrations (aka IC50s) (in nM) of all possible n-mers within a peptide

Usage

predict_ic50s(
  protein_sequence,
  peptide_length,
  mhcnuggets_options,
  peptides_path = create_temp_peptides_path()
)

Arguments

Value

a tibble with columns:

• peptide the peptide fragment, each of length peptide_length

• ic50 the predicted IC50 (in nM)

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_mhcnuggets_installed()) {

  mhcnuggets_options <- create_mhcnuggets_options(
    mhc = "HLA-A02:01"
  )

  predict_ic50s(
    protein_sequence = "AIAACAMLLVCCCCCC",
    peptide_length = 13,
    mhcnuggets_options = mhcnuggets_options
  )
}

Set the MHCnuggets installation state to the desired one

Description

Set the MHCnuggets installation state to the desired one

Usage

set_is_mhcnuggets_installed(
  is_installed,
  verbose = FALSE,
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Set the version of pip.

Description

Set the version of pip to a specific version, by installing that version.

Usage

set_pip_version(version)

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

use upgrade_pip to set pip to the latest version. Use downgrade_pip to set pip to a specific earlier version.

Examples

## Not run: 
  if (is_pip_installed()) {
    set_pip_version("19.0")
  }

## End(Not run)

Convert a standard haplotype name to the MHCnuggets name

Description

Convert a standard haplotype name to the MHCnuggets name. Will stop if this conversion fails.

Usage

to_mhcnuggets_name(mhc)

Arguments

Value

the MHCnuggets name for the haplotype

Author(s)

Richèl J.C. Bilderbeek

Examples

to_mhcnuggets_name("HLA-A*01:01")

Convert one or more standard haplotype name to the MHCnuggets names

Description

Convert one or more standard haplotype names to the MHCnuggets names. Will stop if this conversion fails.

Usage

to_mhcnuggets_names(mhcs)

Arguments

Value

the MHCnuggets names for the haplotypes

Author(s)

Richèl J.C. Bilderbeek

Examples

to_mhcnuggets_names("HLA-A*01:01")

Uninstall the MHCnuggets Python package.

Description

Uninstall the MHCnuggets Python package.

Usage

uninstall_mhcnuggets(
  folder_name = get_default_mhcnuggets_folder(),
  mhcnuggets_url = get_mhcnuggets_url()
)

Arguments

Author(s)

Richèl J.C. Bilderbeek

Install pip.

Description

Install pip.

Usage

uninstall_pip()

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Examples

## Not run: 
  uninstall_pip()

## End(Not run)

Uograde pip.

Description

Uograde pip.

Usage

upgrade_pip()

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

use downgrade_pip to set pip to an earlier version. Use set_pip_version to install a specific version of pip

Examples

## Not run: 
  install_pip()

## End(Not run)