Title:	Predict Transmembrane Protein Topology
Version:	1.4
Description:	Proteins reside in either the cell plasma or in the cell membrane. A membrane protein goes through the membrane at least once. Given the amino acid sequence of a membrane protein, the tool 'PureseqTM' (https://github.com/PureseqTM/pureseqTM_package, as described in "Efficient And Accurate Prediction Of Transmembrane Topology From Amino acid sequence only.", Wang, Qing, et al (2019), <doi:10.1101/627307>), can predict the topology of a membrane protein. This package allows one to use 'PureseqTM' from R.
License:	GPL-3
Encoding:	UTF-8
RoxygenNote:	7.2.3
Depends:	R (≥ 3.5.0)
Imports:	data.table, devtools, dplyr, ggplot2, Peptides, plyr, rappdirs, readr, stringr, tibble, Rcpp
Suggests:	testthat, knitr, markdown, rmarkdown, profvis
URL:	https://github.com/richelbilderbeek/pureseqtmr/
BugReports:	https://github.com/richelbilderbeek/pureseqtmr/
VignetteBuilder:	knitr
SystemRequirements:	PureseqTM (https://github.com/PureseqTM/pureseqTM_package)
LinkingTo:	Rcpp
NeedsCompilation:	yes
Packaged:	2023-04-06 13:18:26 UTC; richel
Author:	Richèl J.C. Bilderbeek [aut, cre]
Maintainer:	Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>
Repository:	CRAN
Date/Publication:	2023-04-06 13:40:02 UTC

Are the sequences transmembrance helices?

Description

Are the sequences transmembrance helices?

Usage

are_tmhs(protein_sequences, folder_name = get_default_pureseqtm_folder())

Arguments

Value

a vector of booleans of the same length as the number of sequences. The ith element is TRUE if the ith protein sequence is a transmembrane helix

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  sequences <- c(
    "QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLM",
    "VVIILTIRGNILVIMAVSLE"
  )
  are_tmhs(sequences)
}

Determine if these are all valid protein sequences

Description

Determine if these are all valid protein sequences, as can be used in topology prediction

Usage

are_valid_protein_sequences(protein_sequences, verbose = FALSE)

Arguments

Value

TRUE if the protein sequence is valid

Calculate the the distance for each amino acid to the center of the TMH

Description

Calculate the the distance for each amino acid to the center of the TMH

Usage

calc_distance_to_tmh_center_from_topology(topology)

Arguments

Value

a tibble with the columns 'name' and 'position' and 'distance_to_tmh_center'

Author(s)

Richèl J.C. Bilderbeek

Calculate the the distance for each amino acid to the center of the TMH

Description

Calculate the the distance for each amino acid to the center of the TMH

Usage

calc_distance_to_tmh_center_from_topology_str(topology_str)

Arguments

Value

a tibble with the columns 'position' and 'distance_to_tmh_center'

Author(s)

Richèl J.C. Bilderbeek

Use Rcpp to calculate the distance to a TMH center

Description

Use Rcpp to calculate the distance to a TMH center

Usage

calc_distance_to_tmh_center_from_topology_str_cpp_stl(topology_str)

Arguments

Value

a vector with distances

Check one protein sequence

Description

Will stop if the protein sequence is invalid, with a helpful error message.

Usage

check_protein_sequence(protein_sequence)

Arguments

Details

A protein sequence is invalid if:

• it has zero, two or more sequences

• the sequence contains zero, 1 or 2 amino acids

• the sequence contains characters that are not in the amino acid uppercase alphabet, that is ACDEFGHIKLMNPQRSTVWY

Value

nothing. Will stop if the protein sequence is invalid, with a helpful error message.

Examples

check_protein_sequence("FAMILYVW")

Check one or more protein sequences

Description

Will stop if the protein sequence is invalid, with a helpful error message.

Usage

check_protein_sequences(protein_sequences)

Arguments

Details

A protein sequence is invalid if:

• it has zero, two or more sequences

• the sequence contains zero, 1 or 2 amino acids

• the sequence contains characters that are not in the amino acid uppercase alphabet, that is ACDEFGHIKLMNPQRSTVWY

Value

nothing. Will stop at the first invalid protein sequence, with a helpful error message.

Examples

check_protein_sequences(c("FAMILYVW", "FAMILYVW"))

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

Description

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

Usage

check_pureseqtm_installation(folder_name = get_default_pureseqtm_folder())

Arguments

Value

Nothing. Will stop with a helpful error message if PureseqTM is not installed.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  check_pureseqtm_installation()
}

Check if the topology is valid.

Description

Check if the argument is of the same type as a predicted topology, as can be created with predict_topology. Will stop if not.

Usage

check_topology(topology)

Arguments

Value

Nothing. Will stop with a helpful error message if the topology is invalid.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  fasta_filename <- get_example_filename("1bhaA.fasta")
  topology <- predict_topology(fasta_filename)
  check_topology(topology)
}

Check if the topology string is valid. Will stop if not.

Description

Check if the topology string is valid. Will stop if not.

Usage

check_topology_str(topology_str)

Arguments

Value

Nothing. Will stop with a helpful error message if the topology is invalid.

Author(s)

Richèl J.C. Bilderbeek

Examples

check_topology_str("0000000000000000000000000011111111111111111100000")

Convert a TMHMM topology to a PureseqTM topology

Description

Convert a TMHMM topology to a PureseqTM topology

Usage

convert_tmhmm_to_pureseqtm_topology(tmhmm_topology)

Arguments

Value

a tibble with column names name and topology, as can be checked by check_topology

Author(s)

Richèl J.C. Bilderbeek

Examples

tmhmm_topo_filename <- system.file(
  "extdata", "UP000005640_9606_no_u.tmhmm", package = "pureseqtmr"
)
tmhmm_topology <- load_topology_file_as_tibble(tmhmm_topo_filename)
convert_tmhmm_to_pureseqtm_topology(tmhmm_topology)

Count the number of TMHs in a topology

Description

Count the number of TMHs in a topology

Usage

count_n_tmhs(topology_strs)

Arguments

Examples

count_n_tmhs("00000000000000000000000000")
count_n_tmhs("00000000001111100000000000")
count_n_tmhs(c("0", "1"))

Create the five PureseqTM output files, by running PureseqTM.

Description

Create the five PureseqTM output files, by running PureseqTM.

Usage

create_pureseqtm_files(
  fasta_filename,
  folder_name = get_default_pureseqtm_folder(),
  temp_folder_name = tempfile(pattern = "pureseqt_")
)

Arguments

Value

full path to the files created

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  fasta_filename <- get_example_filename("1bhaA.fasta")
  create_pureseqtm_files(fasta_filename)
}

Create the output file of a PureseqTM proteome run

Description

Create the output file of a PureseqTM proteome run

Usage

create_pureseqtm_proteome_file(
  fasta_filename,
  topology_filename = tempfile(fileext = ".top"),
  folder_name = get_default_pureseqtm_folder()
)

Arguments

Value

the filename

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  fasta_filename <- get_example_filename("1bhaA.fasta")
  create_pureseqtm_proteome_file(fasta_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(
  download_url,
  fasta_filename,
  fasta_file_text,
  folder_name,
  protein_sequence,
  protein_sequences,
  pureseqtm_filename,
  pureseqtm_proteome_text,
  pureseqtm_result,
  pureseqtm_url,
  temp_fasta_filename,
  temp_folder_name,
  tmhmm_topology,
  topology,
  topology_filename,
  topology_str,
  topology_strs,
  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

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

Description

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

Usage

get_default_pureseqtm_folder()

Value

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

Author(s)

Richèl J.C. Bilderbeek

Examples

get_default_pureseqtm_folder()

Get the full path to a PureseqTM example file.

Description

Get the full path to a PureseqTM example file. If the filename specified is not a PureseqTM example file, this function will stop

Usage

get_example_filename(filename, folder_name = get_default_pureseqtm_folder())

Arguments

Value

the full path to a PureseqTM example file

Author(s)

Richèl J.C. Bilderbeek

See Also

use get_example_filenames to get all PureseqTM example filenames

Examples

if (is_pureseqtm_installed()) {
  get_example_filename("1bhaA.fasta")
}

Get the full path to all PureseqTM example files

Description

Get the full path to all PureseqTM example files

Usage

get_example_filenames(folder_name = get_default_pureseqtm_folder())

Arguments

Value

a character vector with all PureseqTM example files

Author(s)

Richèl J.C. Bilderbeek

See Also

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

Examples

if (is_pureseqtm_installed()) {
  get_example_filenames()
}

Get the URL of the PureseqTM source code

Description

Get the URL of the PureseqTM source code

Usage

get_pureseqtm_url()

Value

a URL as a character vector of one element

Author(s)

Richèl J.C. Bilderbeek

Examples

get_pureseqtm_url()

Get the PureseqTM version

Description

Get the PureseqTM version

Usage

get_pureseqtm_version(folder_name = get_default_pureseqtm_folder())

Arguments

Value

a version number as a character vector of one element, for example v0.10

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  get_pureseqtm_version()
}

Install PureseqTM to a local folder

Description

Install PureseqTM to a local folder

Usage

install_pureseqtm(
  folder_name = get_default_pureseqtm_folder(),
  pureseqtm_url = get_pureseqtm_url()
)

Arguments

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Examples

## Not run: 
  install_pureseqtm()

## End(Not run)

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

Author(s)

Richèl J.C. Bilderbeek

Examples

  if (is_on_ci()) {
    message("Running on a continuous integration service")
  }

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

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")
  }

Is the line of text the name of a protein, as used within a FASTA filename?

Description

Is the line of text the name of a protein, as used within a FASTA filename?

Usage

is_protein_name_line(line)

Arguments

Value

TRUE if the line can be the name of a protein in a FASTA file

Author(s)

Richèl J.C. Bilderbeek

Examples

is_protein_name_line(">5H2A_CRIGR")

Measure if PureseqTM is installed locally

Description

Measure if PureseqTM is installed locally

Usage

is_pureseqtm_installed(folder_name = get_default_pureseqtm_folder())

Arguments

Value

TRUE is PureseqTM is installed locally, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Examples

is_pureseqtm_installed()

Determine if the protein sequence contains at least one transmembrane helix.

Description

Determine if the protein sequence contains at least one transmembrane helix.

Usage

is_tmh(protein_sequence, folder_name = get_default_pureseqtm_folder())

Arguments

Value

TRUE if the protein sequence contains at least one transmembrane helix

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  # This sequence is a TMH
  is_tmh("QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLM")

  # This sequence is not a TMH
  is_tmh("VVIILTIRGNILVIMAVSLE")
}

Is the line of text the topology, as used within a FASTA filename?

Description

Is the line of text the topology, as used within a FASTA filename? In this context, a topology is a string of zeroes and ones, in which a one denotes that that amino acid is within the membrane.

Usage

is_topology_line(line)

Arguments

Value

TRUE if the line can be the text of a topology in a FASTA file.

Author(s)

Richèl J.C. Bilderbeek

Examples

# This is a valid topology
is_topology_line("000010101011")

# This is an invalid topology
is_topology_line("invalid")

Determine if this a valid protein sequence

Description

Determine if this is a valid protein sequence, as can be used in topology prediction

Usage

is_valid_protein_sequence(protein_sequence, verbose = FALSE)

Arguments

Value

TRUE if the protein sequence is valid

Parse a FASTA file to a table with a name and sequence column

Description

Parse a FASTA file to a table with a name and sequence column

Usage

load_fasta_file_as_tibble(fasta_filename)

Arguments

Value

a tibble with a name and sequence column

See Also

use load_fasta_file_as_tibble_cpp to directly call the C++ function that does the actual work. Use load_fasta_file_as_tibble_r to call the (approx ten thousand times slower) R function

Parse a FASTA file to a table with a name and sequence column

Description

Parse a FASTA file to a table with a name and sequence column

Usage

load_fasta_file_as_tibble_cpp(fasta_filename)

Arguments

Value

a tibble with a name and sequence column

Use Rcpp to load a FASTA file

Description

Use Rcpp to load a FASTA file

Usage

load_fasta_file_as_tibble_cpp_raw(fasta_filename)

Arguments

Value

a list with two character vectors, named 'name' and 'sequence'

Parse a FASTA file to a table with a name and sequence column

Description

Parse a FASTA file to a table with a name and sequence column

Usage

load_fasta_file_as_tibble_r(fasta_filename)

Arguments

Value

a tibble with a name and sequence column

Parse a topology (.topo) file to a table with a name and topology column

Description

Parse a topology (.topo) file to a table with a name and topology column

Usage

load_topology_file_as_tibble(topology_filename)

Arguments

Value

a tibble with a name and topology column, as can be checked by check_topology

Examples

topology_filename <- system.file(
 "extdata", "100507436.topo", package = "pureseqtmr"
)
load_topology_file_as_tibble(topology_filename)

Do a mock prediction directy on a protein sequence, as can be useful in testing Use predict_topologies_from_sequences for doing a real prediction.

Description

Do a mock prediction directy on a protein sequence, as can be useful in testing Use predict_topologies_from_sequences for doing a real prediction.

Usage

mock_predict_topologies_from_sequences(protein_sequences)

Arguments

Value

a topology as a string of zeroes and ones, where a one denotes that the corresponding amino acid is located within the membrane.

Author(s)

Richèl J.C. Bilderbeek

Examples

protein_sequence <- paste0(
  "QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLM",
  "SLAIADMLLGFLVMPVSMLTILYGYRWP"
)
mock_predict_topologies_from_sequences(protein_sequence)

Do a mock prediction of the topology of proteins

Description

Uses predict_topology for doing a real prediction

Usage

mock_predict_topology(fasta_filename)

Arguments

Value

a tibble with the columns 'name' and 'topology', where the 'name' column hold all the proteins' names, and 'topology' contains all respective topologies.

Author(s)

Richèl J.C. Bilderbeek

Examples

fasta_filename <- tempfile()
save_tibble_as_fasta_file(
  t = tibble::tibble(
    name = c("A", "B"),
    sequence = c("FAMILYVW", "VWFAMILY")
  ),
  fasta_filename = fasta_filename
)
mock_predict_topology(fasta_filename)

Parse the output of a call to PureseqTM_proteome.sh

Description

Parse the output of a call to PureseqTM_proteome.sh

Usage

parse_pureseqtm_proteome_text(pureseqtm_proteome_text)

Arguments

Plot the topology

Description

Plot the topology

Usage

plot_topology(topology)

Arguments

Value

a ggplot that displays the topology of one or more proteins

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed() && is_on_ci()) {
  fasta_filename <- get_example_filename("test_proteome.fasta")
  topology <- predict_topology(fasta_filename)
  plot_topology(topology)
}

Run PureseqTM directy on a protein sequence

Description

Run PureseqTM directy on a protein sequence

Usage

predict_topologies_from_sequences(
  protein_sequences,
  folder_name = get_default_pureseqtm_folder(),
  temp_fasta_filename = tempfile(fileext = ".fasta")
)

Arguments

Value

a topology as a string of zeroes and ones, where a one denotes that the corresponding amino acid is located within the membrane.

Author(s)

Richèl J.C. Bilderbeek

See Also

use mock_predict_topologies_from_sequences to mock the prediction of protein sequences, as can be useful in testing

Examples

if (is_pureseqtm_installed()) {
  protein_sequence <- paste0(
    "QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLM",
    "SLAIADMLLGFLVMPVSMLTILYGYRWP"
  )
  predict_topology_from_sequence(protein_sequence)
}

Predict the topology of proteins from file

Description

Predict the topology of zero, one or more proteins, of which the names and sequences are stored in the FASTA format

Usage

predict_topology(
  fasta_filename,
  folder_name = get_default_pureseqtm_folder(),
  topology_filename = tempfile(fileext = ".top")
)

Arguments

Value

a tibble with the columns 'name' and 'topology', where the 'name' column hold all the proteins' names, and 'topology' contains all respective topologies.

Note

unlike PureseqTM, the topologies predicted are returned in the same order as the original sequences. A bugreport is posted at the PureseqTM GitHub repository at https://github.com/PureseqTM/PureseqTM_Package/issues/11

Author(s)

Richèl J.C. Bilderbeek

See Also

use mock_predict_topology to do a mock prediction, as can be useful in testing

Examples

if (is_pureseqtm_installed()) {
  fasta_filename <- get_example_filename("1bhaA.fasta")
  predict_topology(fasta_filename)
}

Run PureseqTM directy on a protein sequence

Description

Will stop if the protein sequence is shorter than three amino acids.

Usage

predict_topology_from_sequence(
  protein_sequence,
  folder_name = get_default_pureseqtm_folder(),
  temp_fasta_filename = tempfile(fileext = ".fasta")
)

Arguments

Value

a topology as a string of zeroes and ones, where a one denotes that the corresponding amino acid is located within the membrane.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  protein_sequence <- paste0(
    "QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLM",
    "SLAIADMLLGFLVMPVSMLTILYGYRWP"
  )
  predict_topology_from_sequence(protein_sequence)
}

pureseqtmr: 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_pureseqtm_installed()) {
  # Obtain an example filename
  fasta_filename <- get_example_filename("1bhaA.fasta")

  # Get the topology as a tibble
  topology <- predict_topology(fasta_filename)

  # show the topology
  plot_topology(topology)
}

Create a pureseqtmr report, to be used when reporting bugs

Description

Create a pureseqtmr report, to be used when reporting bugs

Usage

pureseqtmr_report(folder_name = get_default_pureseqtm_folder())

Arguments

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Examples

pureseqtmr_report()

Run PureseqTM on a proteome

Description

Run PureseqTM on a proteome

Usage

run_pureseqtm_proteome(
  fasta_filename,
  folder_name = get_default_pureseqtm_folder(),
  topology_filename = tempfile(fileext = ".top")
)

Arguments

Value

the topology of the proteome, using the same output as PureseqTM. Use predict_topology to get the topology as a tibble

Author(s)

Richèl J.C. Bilderbeek

See Also

• Use predict_topology to predict the topology of a proteome

• Use create_pureseqtm_files to only create the PureseqTM output files

Examples

if (is_pureseqtm_installed()) {
  fasta_filename <- get_example_filename("1bhaA.fasta")
  run_pureseqtm_proteome(fasta_filename)
}

Save the first two columns of a tibble as a FASTA file

Description

Save the first two columns of a tibble as a FASTA file

Usage

save_tibble_as_fasta_file(t, fasta_filename)

Arguments

Author(s)

Richèl J.C. Bilderbeek

Count the number of transmembrane helices in a topology

Description

Count the number of transmembrane helices in a topology

Usage

tally_tmhs(topology)

Arguments

Value

a tibble with the number of TMHs per protein

Examples

if (is_pureseqtm_installed()) {
  tally_tmhs(
    predict_topology(
      get_example_filename("1bhaA.fasta")
    )
  )
}

Uninstall PureseqTM

Description

Uninstall PureseqTM

Usage

uninstall_pureseqtm(folder_name = get_default_pureseqtm_folder())

Arguments

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek