Title:	Interface to 'NetMHCIIpan'
Version:	1.3.2
Maintainer:	Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>
Description:	The field of immunology benefits from software that can predict which peptide sequences trigger an immune response. 'NetMHCIIpan' is a such a tool: it predicts the binding strength of a short peptide to a Major Histocompatibility Complex class II (MHC-II) molecule. 'NetMHCIIpan' can be used from a web server at https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/ or from the command-line, using a local installation. This package allows to call 'NetMHCIIpan' from R.
License:	GPL-3
Encoding:	UTF-8
Imports:	devtools, dplyr, rappdirs, readr, seqinr, stringr, testit, tibble
Suggests:	knitr, rmarkdown, testthat, spelling
VignetteBuilder:	knitr
RoxygenNote:	7.2.3
Language:	en-US
URL:	https://github.com/richelbilderbeek/netmhc2pan/
BugReports:	https://github.com/richelbilderbeek/netmhc2pan/issues
SystemRequirements:	NetMHC2pan (https://services.healthtech.dtu.dk/service.php?NetMHCIIpan-3.2)
NeedsCompilation:	no
Packaged:	2023-11-08 16:05:13 UTC; richel
Author:	Richèl J.C. Bilderbeek [aut, cre], Lue Ping Zhao [ctb], Byungkuk Min [ctb]
Repository:	CRAN
Date/Publication:	2023-11-08 23:10:07 UTC

Convert the first character to upper case.

Description

Convert the first character to upper case. If the first character is upper case, nothing will happen.

Usage

capitalize_first_char(s)

Arguments

Value

the string, with the first letter in uppercase

Author(s)

Richèl J.C. Bilderbeek

Examples

capitalize_first_char("hello")

Check the allele names

Description

Check if the alleles have a valid NetMHC2pan name. Will stop if not.

Usage

check_alleles(
  alleles,
  netmhc2pan_folder_name = get_default_netmhc2pan_folder()
)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use to_netmhc2pan_name to convert a formal name to an NetMHC2pan name. Use get_netmhc2pan_alleles for a list of all supported alleles (in NetMHC2pan naming format).

Examples

if (is_netmhc2pan_installed()) {
  check_alleles("DRB1_0101")
  check_alleles(c("DRB1_0102", "DRB1_0103"))
}

Check that a file can be created at a certain path.

Description

Will stop if not. Will stop if the file already exists. Does so by creating an empty file at the path, and then deleting it.

Usage

check_can_create_file(filename, overwrite = TRUE)

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Check the lengths of the sequences in a FASTA file

Description

Check if the lengths of the sequences in a FASTA file are at least equal to the desired peptide lengths.

Usage

check_fasta_file_sequence_lengths(fasta_filename, peptide_length)

Arguments

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Examples

# FASTA file in which all proteons have a length of at keast 13
fasta_filename <- system.file(
  "extdata", "example.fasta", package = "netmhc2pan"
)
check_fasta_file_sequence_lengths(
  fasta_filename = fasta_filename,
  peptide_length = 13
)

Check the URL of the NetMHCIIpan binary tarball

Description

Check the URL of the NetMHCIIpan binary tarball is valid, will stop if not. This URL link expires after 4 hours.

Usage

check_netmhc2pan_bin_url(
  netmhc2pan_bin_url = get_netmhc2pan_bin_url(),
  verbose = FALSE,
  netmhc2pan_archive_filename = get_netmhc2pan_archive_filename(),
  temp_local_file = tempfile(pattern = "check_netmhc2pan_bin_url_")
)

Arguments

Value

Nothing

Check the URL of the NetMHCIIpan binary tarball

Description

Check the URL of the NetMHCIIpan binary tarball is valid, will stop if not. This URL link expires after 4 hours.

Usage

check_netmhc2pan_data_url(
  netmhc2pan_data_url = get_netmhc2pan_data_url(),
  verbose = FALSE,
  temp_local_file = tempfile(pattern = "check_netmhc2pan_data_url_")
)

Arguments

Value

Nothing

Checks the installation of NetMHCIIpan.

Description

Checks the installation of NetMHCIIpan. Throws a helpful error message if incomplete, else does nothing

Usage

check_netmhc2pan_installation(
  netmhc2pan_folder_name = get_default_netmhc2pan_folder()
)

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Examples

# Will stop if NetMHC2pan is not installed
try(check_netmhc2pan_installation())

Create a .fasta file

Description

Create a .fasta file

Usage

create_temp_fasta_filename()

Value

a path to a non-existing file, for example, /home/myusername/.cache/temp_582046426735.fasta

Author(s)

Richèl J.C. Bilderbeek

Examples

create_temp_fasta_filename()

Create a .xls file

Description

Create a .xls file

Usage

create_temp_xls_filename()

Value

a path to a non-existing file, for example, /home/myusername/.cache/temp_582047dac733.xls

Author(s)

Richèl J.C. Bilderbeek

Examples

create_temp_xls_filename()

This function does nothing. It is intended to inherit is parameters' documentation.

Description

This function does nothing. It is intended to inherit is parameters' documentation.

Usage

default_params_doc(
  alleles,
  do_filter,
  fasta_filename,
  folder_name,
  mhc_haplotype,
  netmhc2pan_archive_filename,
  netmhc2pan_bin_tarfile_path,
  netmhc2pan_bin_url,
  netmhc2pan_data_tarfile_path,
  netmhc2pan_data_url,
  netmhc2pan_folder_name,
  netmhc2pan_subfolder,
  netmhc2pan_version,
  os,
  peptide_length,
  peptides,
  protein_sequence,
  temp_fasta_filename,
  temp_local_file,
  temp_xls_filename,
  verbose,
  xls_filename
)

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

Download the NetMHCIIpan binary

Description

Download the NetMHCIIpan binary tarball file

Usage

download_netmhc2pan_bin(
  netmhc2pan_bin_url = get_netmhc2pan_bin_url(),
  netmhc2pan_bin_tarfile_path = get_default_netmhc2pan_bin_tarfile_path(),
  verbose = FALSE,
  netmhc2pan_archive_filename = get_netmhc2pan_archive_filename(),
  temp_local_file = tempfile(pattern = "netmhc2pan_download_netmhc2pan_")
)

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Get the full path to the default NetMHC2pan binary

Description

Get the full path to the default NetMHC2pan binary

Usage

get_default_netmhc2pan_bin_path(
  netmhc2pan_subfolder = get_default_netmhc2pan_subfolder()
)

Arguments

Value

the full path to the default NetMHC2pan binary

Author(s)

Richèl J.C. Bilderbeek

Examples

get_default_netmhc2pan_bin_path()

Get the default path for the NetMHCIIpan binary tarball file

Description

Get the default path for the NetMHCIIpan binary tarball file. This is the location where it will be saved to after downloading.

Usage

get_default_netmhc2pan_bin_tarfile_path(
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  netmhc2pan_archive_filename = get_netmhc2pan_archive_filename()
)

Arguments

Value

the default path for the NetMHCIIpan binary tarball file

Author(s)

Richèl J.C. Bilderbeek

Examples

get_default_netmhc2pan_bin_tarfile_path()

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

Description

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

Usage

get_default_netmhc2pan_folder()

Value

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

Author(s)

Richèl J.C. Bilderbeek

Examples

get_default_netmhc2pan_folder()

Get the full path to the NetMHC2pan sub-folder

Description

Get the full path to the NetMHC2pan sub-folder

Usage

get_default_netmhc2pan_subfolder(
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  netmhc2pan_version = get_default_netmhc2pan_version()
)

Arguments

Value

the full path to the NetMHC2pan sub-folder

Author(s)

Richèl J.C. Bilderbeek

Examples

get_default_netmhc2pan_subfolder()

Get the default NetMHC2pan version used

Description

Get the default NetMHC2pan version used

Usage

get_default_netmhc2pan_version()

Value

the default NetMHC2pan version used

Author(s)

Richèl J.C. Bilderbeek

Examples

get_default_netmhc2pan_version()

Get a list of the alleles supported by NetMHCIIpan

Description

Get a list of the alleles supported by NetMHCIIpan

Usage

get_netmhc2pan_alleles(
  netmhc2pan_folder_name = get_default_netmhc2pan_folder()
)

Arguments

Value

a character vector with the NetMHCIIpan alleles

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_netmhc2pan_installed()) {
  get_netmhc2pan_alleles()[1:5]
}

Get the filename of the NetMHC2pan archive file

Description

Get the filename of the NetMHC2pan archive file

Usage

get_netmhc2pan_archive_filename(
  netmhc2pan_version = get_default_netmhc2pan_version()
)

Arguments

Value

the filename of the NetMHC2pan archive file

Examples

get_netmhc2pan_archive_filename()

Get the NetMHCIIpan binary download URL.

Description

Get the URL for the NetMHCIIpan binary, as is emailed. These expire after 4 hours.

Usage

get_netmhc2pan_bin_url()

Value

a download URL

Author(s)

Richèl J.C. Bilderbeek

See Also

Use is_url_valid to determine if the download URL is still valid. Use check_netmhc2pan_bin_url to get a helpful error message if this URL is invalid.

Get the NetMHCIIpan data tarball URL.

Description

Get the NetMHCIIpan data tarball URL.

Usage

get_netmhc2pan_data_url()

Value

a download URL

Author(s)

Richèl J.C. Bilderbeek

See Also

Use is_url_valid to determine if the download URL is still valid. Use check_netmhc2pan_data_url to get a helpful error message if this URL is invalid.

Deprecated, use get_netmhc2pan_bin_url instead

Description

Deprecated, use get_netmhc2pan_bin_url instead

Usage

get_netmhc2pan_url()

Value

a download URL

Author(s)

Richèl J.C. Bilderbeek

Install NetMHCIIpan

Description

Install NetMHCIIpan to a local folder, by downloading the binary and data files. Use install_netmhc2pan_from_files to install NetMHCIIpan from files that are already downloaded.

Usage

install_netmhc2pan(
  netmhc2pan_bin_url = get_netmhc2pan_bin_url(),
  netmhc2pan_data_url = get_netmhc2pan_data_url(),
  verbose = FALSE,
  netmhc2pan_archive_filename = get_netmhc2pan_archive_filename(),
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  temp_local_file = tempfile(pattern = "netmhc2pan_install_netmhc2pan_")
)

Arguments

Details

These are three steps:

• Install the NetMHCIIpan binary, using install_netmhc2pan_bin

• Install the NetMHCIIpan data, using install_netmhc2pan_data

• Set up NetMHCIIpan, using set_up_netmhc2pan

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Install the NetMHCIIpan binary to a local folder

Description

Install the NetMHCIIpan binary to a local folder.

Usage

install_netmhc2pan_bin(
  netmhc2pan_bin_url = get_netmhc2pan_bin_url(),
  verbose = FALSE,
  netmhc2pan_archive_filename = get_netmhc2pan_archive_filename(),
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  temp_local_file = tempfile(pattern = "netmhc2pan_install_netmhc2pan_bin_")
)

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Install the NetMHCIIpan binary to a local folder

Description

Install the NetMHCIIpan binary to a local folder

Usage

install_netmhc2pan_bin_from_file(
  netmhc2pan_bin_tarfile_path,
  verbose = FALSE,
  netmhc2pan_archive_filename = get_netmhc2pan_archive_filename(),
  netmhc2pan_folder_name = get_default_netmhc2pan_folder()
)

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Install the NetMHCIIpan data to a local folder

Description

Install the NetMHCIIpan data to a local folder.

Usage

install_netmhc2pan_data(
  netmhc2pan_data_url = get_netmhc2pan_data_url(),
  netmhc2pan_folder_name = rappdirs::user_data_dir(),
  verbose = FALSE
)

Arguments

Details

This data can be downloaded from https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/data.Linux.tar.gz, without filling in a contact form.

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Install the NetMHCIIpan data from file

Description

Install the NetMHCIIpan data from the NetMHCIIpan data tarball file to the default NetMHCIIpan folder.

Usage

install_netmhc2pan_data_from_file(
  netmhc2pan_data_tarfile_path,
  netmhc2pan_folder_name = rappdirs::user_data_dir(),
  verbose = FALSE
)

Arguments

Details

The NetMHCIIpan data tarball file can be in any path.

The data tarball file can be downloaded from https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/data.Linux.tar.gz, without filling in a contact form.

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Install NetMHCIIpan from files.

Description

Install NetMHCIIpan to a local folder from (already downloaded) binary and date tarball files. Use install_netmhc2pan to install NetMHCIIpan by downloading these files

Usage

install_netmhc2pan_from_files(
  netmhc2pan_bin_tarfile_path,
  netmhc2pan_data_tarfile_path,
  verbose = FALSE,
  netmhc2pan_archive_filename = get_netmhc2pan_archive_filename(),
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  temp_local_file = tempfile(pattern = "netmhc2pan_install_netmhc2pan_")
)

Arguments

Details

These are three steps:

• Install the NetMHCIIpan binary, using install_netmhc2pan_bin_from_file

• Install the NetMHCIIpan data, using install_netmhc2pan_data_from_file

• Set up NetMHCIIpan, using set_up_netmhc2pan

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Measure if NetMHCIIpan binary is installed locally

Description

Measure if NetMHCIIpan binary is installed locally

Usage

is_netmhc2pan_bin_installed(
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  verbose = FALSE
)

Arguments

Value

TRUE is NetMHCIIpan binary is installed locally, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Measure if NetMHCIIpan data folder is installed locally

Description

Measure if NetMHCIIpan data folder is installed locally

Usage

is_netmhc2pan_data_installed(
  netmhc2pan_folder_name = get_default_netmhc2pan_folder()
)

Arguments

Value

TRUE is NetMHCIIpan data folder is installed locally, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Is the haplotype valid?

Description

Determines if a haplotype has the same notation as a NetMHC2pan haplotype

Usage

is_netmhc2pan_haplotype(mhc_haplotype)

Arguments

Value

TRUE if the haplotype is a valid NetMHCIIpan haplotype

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_netmhc2pan_installed()) {
  is_netmhc2pan_haplotype("DRB1_0311")
  is_netmhc2pan_haplotype("nonsense")
}

Measure if NetMHCIIpan is installed locally

Description

Measure if NetMHCIIpan is installed locally

Usage

is_netmhc2pan_installed(
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  verbose = FALSE
)

Arguments

Value

TRUE is NetMHCIIpan is installed locally, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Measure if NetMHCIIpan is set up

Description

Measure if NetMHCIIpan is set up

Usage

is_netmhc2pan_set_up(netmhc2pan_folder_name = get_default_netmhc2pan_folder())

Arguments

Value

TRUE is NetMHCIIpan is set up locally, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

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

  if (is_on_appveyor()) {
    message("Running 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

Note

It is possible to fake being on continuous integration service, in this case GitHub Actions, using:

“'r Sys.setenv(GITHUB_ACTIONS = "I fake being on GitHub Actions") is_on_ci() # Will be true “'

To undo this, do

“'r Sys.setenv(GITHUB_ACTIONS = "") is_on_ci() # Will be false “'

Author(s)

Richèl J.C. Bilderbeek

Examples

is_on_ci()

Determines if the environment is GitHub Actions

Description

Determines if the environment is GitHub Actions

Usage

is_on_github_actions()

Value

TRUE if run on GitHub Actions, FALSE otherwise

Note

It is possible to fake being on GitHub Actions, using:

“'r Sys.setenv(GITHUB_ACTIONS = "I fake being on GitHub Actions") is_on_github_actions() # Will be true “'

To undo this, do

“'r Sys.setenv(GITHUB_ACTIONS = "") is_on_github_actions() # Will be false “'

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_github_actions()) {
  message("Running on GitHub Actions")
}

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

  if (is_on_ci()) {
    message("Running on Travis CI")
  }

See if tcsh is installed

Description

See if tcsh is installed

Usage

is_tcsh_installed()

Value

TRUE is tcsh is installed, FALSE otherwise

Note

To install tcsh under Linux, do sudo apt install tcsh

Author(s)

Richèl J.C. Bilderbeek

Is the download URL valid?

Description

The download link expires after 4 hours.

Usage

is_url_valid(
  netmhc2pan_bin_url = get_netmhc2pan_bin_url(),
  verbose = FALSE,
  netmhc2pan_archive_filename = get_netmhc2pan_archive_filename(),
  temp_local_file = tempfile(pattern = "netmhc2pan_is_url_valid_")
)

Arguments

Value

TRUE if the download URL valid, FALSE otherwise

netmhc2pan: predict peptide binding strengths using NetMHC2pan

Description

'NetMHCIIpan' is a tool to predict the binding strength of a short peptide to an MHC-II complex. 'NetMHCIIpan' can be used from a web server at 'https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/' or from the command-line, using a local installation. This package allows to call 'NetMHCIIpan' from R.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_netmhc2pan_installed()) {

  predict_ic50(
    peptides = c("AIAACAMLLV", "ALVCYIVMPV"),
    mhc_haplotype = "DRB1_0416"
  )
}

Show a netmhc2pan report using message, to be used when reporting bugs

Description

Show a netmhc2pan report using message, to be used when reporting bugs

Usage

netmhc2pan_report(netmhc2pan_folder_name = get_default_netmhc2pan_folder())

Arguments

Value

Nothing, it is called for its side effects

Author(s)

Richèl J.C. Bilderbeek

Examples

netmhc2pan_report()

Test NetMHCIIpan by doing a minimal run.

Description

Test NetMHCIIpan by doing a minimal run.

Usage

netmhc2pan_self_test(
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  verbose = FALSE
)

Arguments

Value

Nothing. If the self-test fails, an error will be raised

Author(s)

Richèl J.C. Bilderbeek

Predict the IC50 for peptides.

Description

Predict the half maximal inhibitory concentration (aka IC50) (in nM) for one or more peptides, where the peptides are used as-is, instead of split into smaller peptides. Each peptide must be 15 amino acids at most (use predict_ic50s to predict the IC50s for longer peptides)

Usage

predict_ic50(
  peptides,
  mhc_haplotype,
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  temp_fasta_filename = netmhc2pan::create_temp_fasta_filename(),
  temp_xls_filename = netmhc2pan::create_temp_xls_filename()
)

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 NetMHC2pan reads its input from file. This temporary file is deleted after this function passed successfully.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_netmhc2pan_installed()) {

  predict_ic50(
    peptides = c("AIAACAMLLV", "ALVCYIVMPV"),
    mhc_haplotype = "DRB1_0416"
  )
}

Predict the IC50s from a sequence

Description

Predict the IC50s from a sequence

Usage

predict_ic50s(
  protein_sequence,
  peptide_length,
  mhc_haplotype,
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  temp_fasta_filename = netmhc2pan::create_temp_fasta_filename(),
  temp_xls_filename = netmhc2pan::create_temp_xls_filename()
)

Arguments

Value

a tibble with columns:

• peptide the peptide fragment, each of length peptide_length

• ic50 the predicted IC50 (in nM)

The number of rows equals protein_sequence - peptide_length + 1.

Read MHC2pan output

Description

Read the output produced by MHC2pan, which is an XLS file by default.

Usage

read_netmhc2pan_xls_output(xls_filename)

Arguments

Value

a table

Examples

xls_filename <- system.file("extdata", "example.xls", package = "netmhc2pan")
read_netmhc2pan_xls_output(xls_filename)

Run NetMHCIIpan

Description

Run NetMHCIIpan

Usage

run_netmhc2pan(
  fasta_filename,
  alleles = "DRB1_0101",
  peptide_length = 15,
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  temp_xls_filename = netmhc2pan::create_temp_xls_filename()
)

Arguments

Value

a data frame with the NetMHCIIpan results

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_netmhc2pan_installed()) {

  fasta_filename <- system.file(
    "extdata", "example.fasta", package = "netmhc2pan"
  )
  run_netmhc2pan(fasta_filename)

  # Two alleles
  alleles <- c("DRB1_0101", "DRB1_0102")
  # Run NetMHCpan with these two alleles
  run_netmhc2pan(fasta_filename, alleles = alleles)
}

Install the NetMHCIIpan binary to a local folder

Description

Install the NetMHCIIpan binary to a local folder

Usage

set_up_netmhc2pan(
  netmhc2pan_folder_name = get_default_netmhc2pan_folder(),
  verbose = FALSE
)

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek

Convert a formal haplotype name to its NetMHC2pan notation

Description

Convert a formal MHC-II haplotype name to the notation used by NetMHC2pan.

Usage

to_netmhc2pan_name(mhc_haplotype)

Arguments

Value

the haplotype name in NetMHC2pan notation

Examples

to_netmhc2pan_name("HLA-DRB1*0101")
to_netmhc2pan_name("HLA-DQA1*0501/DQB1*0201")

Uninstall NetMHCIIpan

Description

Uninstall NetMHCIIpan

Usage

uninstall_netmhc2pan(netmhc2pan_folder_name = get_default_netmhc2pan_folder())

Arguments

Value

Nothing

Author(s)

Richèl J.C. Bilderbeek