Package 'pureseqtmr' reference manual

Title:	Predict Transmembrane Protein Topology
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.
Authors:	Richèl J.C. Bilderbeek [aut, cre]
Maintainer:	Richèl J.C. Bilderbeek <[email protected]>
License:	GPL-3
Version:	1.4
Built:	2024-10-31 04:21:13 UTC
Source:	https://github.com/richelbilderbeek/pureseqtmr

Are the sequences transmembrance helices?

Description

Are the sequences transmembrance helices?

Usage

are_tmhs(protein_sequences, folder_name = get_default_pureseqtm_folder())
are_tmhs(protein_sequences, folder_name = get_default_pureseqtm_folder())

Arguments

`protein_sequences`	one ore more protein sequence, each sequence with the amino acids as capitals, for example `MEILCEDNTSLSSIPNSL`
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder

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)
}
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)
are_valid_protein_sequences(protein_sequences, verbose = FALSE)

Arguments

`protein_sequences`	one ore more protein sequence, each sequence with the amino acids as capitals, for example `MEILCEDNTSLSSIPNSL`
`verbose`	set to TRUE for more output

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)
calc_distance_to_tmh_center_from_topology(topology)

Arguments

topology

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

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)
calc_distance_to_tmh_center_from_topology_str(topology_str)

Arguments

topology_str

the topology as a string, for example 000000111100000

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)
calc_distance_to_tmh_center_from_topology_str_cpp_stl(topology_str)

Arguments

topology_str

a topology as a string

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)
check_protein_sequence(protein_sequence)

Arguments

protein_sequence

a protein sequence, with the amino acids as capitals, for example MEILCEDNTSLSSIPNSL. Use check_protein_sequence to check if a protein sequence is valid.

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_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)
check_protein_sequences(protein_sequences)

Arguments

protein_sequences

one ore more protein sequence, each sequence with the amino acids as capitals, for example MEILCEDNTSLSSIPNSL

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"))
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())
check_pureseqtm_installation(folder_name = get_default_pureseqtm_folder())

Arguments

folder_name

superfolder of PureseqTM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_pureseqtm_folder

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()
}
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)
check_topology(topology)

Arguments

topology

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

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)
}
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)
check_topology_str(topology_str)

Arguments

topology_str

the topology as a string, for example 000000111100000

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")
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)
convert_tmhmm_to_pureseqtm_topology(tmhmm_topology)

Arguments

tmhmm_topology

topology as used by TMHMM

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)
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)
count_n_tmhs(topology_strs)

Arguments

topology_strs

the topologies as zero, one oor more strings, for example c("0", "1")

Examples

count_n_tmhs("00000000000000000000000000")
count_n_tmhs("00000000001111100000000000")
count_n_tmhs(c("0", "1"))
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_")
)
create_pureseqtm_files(
  fasta_filename,
  folder_name = get_default_pureseqtm_folder(),
  temp_folder_name = tempfile(pattern = "pureseqt_")
)

Arguments

`fasta_filename`	path to a FASTA file
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder
`temp_folder_name`	path of a temporary folder. The folder does not need to exist. Files that are out in this folder are not automatically deleted, which is not a problem, as the default path given by tempdir is automatically cleaned by the operating system

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

Arguments

`fasta_filename`	path to a FASTA file
`topology_filename`	name of the file to save a protein's topology to
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder

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)
}
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
)
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

`download_url`	the URL to download PureseqTM from
`fasta_filename`	path to a FASTA file
`fasta_file_text`	text of a FASTA file
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder
`protein_sequence`	a protein sequence, with the amino acids as capitals, for example `MEILCEDNTSLSSIPNSL`. Use check_protein_sequence to check if a protein sequence is valid.
`protein_sequences`	one ore more protein sequence, each sequence with the amino acids as capitals, for example `MEILCEDNTSLSSIPNSL`
`pureseqtm_filename`	filename to write the PureseqTM results to
`pureseqtm_proteome_text`	the output of a call to `PureseqTM_proteome.sh`
`pureseqtm_result`	the result of a PureseqTM run
`pureseqtm_url`	URL of the PureseqTM git repository
`temp_fasta_filename`	temporary FASTA filename, which will deleted after usage
`temp_folder_name`	path of a temporary folder. The folder does not need to exist. Files that are out in this folder are not automatically deleted, which is not a problem, as the default path given by tempdir is automatically cleaned by the operating system
`tmhmm_topology`	topology as used by `TMHMM`
`topology`	the topology as a tibble with the columns 'name' and 'topology', where the 'name' column hold all the proteins' names, and 'topology' contains the respective topologies as strings.
`topology_filename`	name of the file to save a protein's topology to
`topology_str`	the topology as a string, for example `000000111100000`
`topology_strs`	the topologies as zero, one oor more strings, for example `c("0", "1")`
`verbose`	set to TRUE for more output

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()
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_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())
get_example_filename(filename, folder_name = get_default_pureseqtm_folder())

Arguments

`filename`	name of the example file, without the path
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder

Value

the full path to a PureseqTM example file

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  get_example_filename("1bhaA.fasta")
}
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())
get_example_filenames(folder_name = get_default_pureseqtm_folder())

Arguments

folder_name

superfolder of PureseqTM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_pureseqtm_folder

Value

a character vector with all PureseqTM example files

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_pureseqtm_installed()) {
  get_example_filenames()
}
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()
get_pureseqtm_url()

Value

a URL as a character vector of one element

Author(s)

Richèl J.C. Bilderbeek

Examples

get_pureseqtm_url()
get_pureseqtm_url()

Get the PureseqTM version

Description

Get the PureseqTM version

Usage

get_pureseqtm_version(folder_name = get_default_pureseqtm_folder())
get_pureseqtm_version(folder_name = get_default_pureseqtm_folder())

Arguments

folder_name

superfolder of PureseqTM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_pureseqtm_folder

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

Arguments

`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder
`pureseqtm_url`	URL of the PureseqTM git repository

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Examples

## Not run: 
  install_pureseqtm()

## End(Not run)
## Not run: 
  install_pureseqtm()

## End(Not run)

Determines if the environment is AppVeyor

Description

Determines if the environment is AppVeyor

Usage

is_on_appveyor()
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")
  }
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()
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")
  }
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()
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")
  }
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()
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")
  }
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)
is_protein_name_line(line)

Arguments

line

line of text from a FASTA filename

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")
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())
is_pureseqtm_installed(folder_name = get_default_pureseqtm_folder())

Arguments

folder_name

superfolder of PureseqTM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_pureseqtm_folder

Value

TRUE is PureseqTM is installed locally, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Examples

is_pureseqtm_installed()
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())
is_tmh(protein_sequence, folder_name = get_default_pureseqtm_folder())

Arguments

`protein_sequence`	a protein sequence, with the amino acids as capitals, for example `MEILCEDNTSLSSIPNSL`. Use check_protein_sequence to check if a protein sequence is valid.
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder

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")
}
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)
is_topology_line(line)

Arguments

line

line of text from a FASTA filename

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")
# 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)
is_valid_protein_sequence(protein_sequence, verbose = FALSE)

Arguments

`protein_sequence`	a protein sequence, with the amino acids as capitals, for example `MEILCEDNTSLSSIPNSL`. Use check_protein_sequence to check if a protein sequence is valid.
`verbose`	set to TRUE for more output

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)
load_fasta_file_as_tibble(fasta_filename)

Arguments

fasta_filename

path to a FASTA file

Value

a tibble with a name and sequence column

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)
load_fasta_file_as_tibble_cpp(fasta_filename)

Arguments

fasta_filename

path to a FASTA file

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)
load_fasta_file_as_tibble_cpp_raw(fasta_filename)

Arguments

fasta_filename

FASTA filename

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)
load_fasta_file_as_tibble_r(fasta_filename)

Arguments

fasta_filename

path to a FASTA file

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)
load_topology_file_as_tibble(topology_filename)

Arguments

topology_filename

name of the file to save a protein's topology to

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)
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)
mock_predict_topologies_from_sequences(protein_sequences)

Arguments

protein_sequences

one ore more protein sequence, each sequence with the amino acids as capitals, for example MEILCEDNTSLSSIPNSL

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)
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)
mock_predict_topology(fasta_filename)

Arguments

fasta_filename

path to a FASTA file

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)
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)
parse_pureseqtm_proteome_text(pureseqtm_proteome_text)

Arguments

pureseqtm_proteome_text

the output of a call to PureseqTM_proteome.sh

Plot the topology

Description

Plot the topology

Usage

plot_topology(topology)
plot_topology(topology)

Arguments

topology

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

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

Arguments

`protein_sequences`	one ore more protein sequence, each sequence with the amino acids as capitals, for example `MEILCEDNTSLSSIPNSL`
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder
`temp_fasta_filename`	temporary FASTA filename, which will deleted after usage

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

Arguments

`fasta_filename`	path to a FASTA file
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder
`topology_filename`	name of the file to save a protein's topology to

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

Examples

if (is_pureseqtm_installed()) {
  fasta_filename <- get_example_filename("1bhaA.fasta")
  predict_topology(fasta_filename)
}
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")
)
predict_topology_from_sequence(
  protein_sequence,
  folder_name = get_default_pureseqtm_folder(),
  temp_fasta_filename = tempfile(fileext = ".fasta")
)

Arguments

`protein_sequence`	a protein sequence, with the amino acids as capitals, for example `MEILCEDNTSLSSIPNSL`
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder
`temp_fasta_filename`	temporary FASTA filename, which will deleted after usage

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)
}
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)
}
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())
pureseqtmr_report(folder_name = get_default_pureseqtm_folder())

Arguments

folder_name

superfolder of PureseqTM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_pureseqtm_folder

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Examples

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

Arguments

`fasta_filename`	path to a FASTA file
`folder_name`	superfolder of PureseqTM. The superfolder's name is `/home/[user_name]/.local/share` by default, as can be obtained by get_default_pureseqtm_folder
`topology_filename`	name of the file to save a protein's topology to

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

Examples

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

Arguments

`t`	a tibble
`fasta_filename`	path to a FASTA file

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)
tally_tmhs(topology)

Arguments

topology

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

Value

a tibble with the number of TMHs per protein

Examples

if (is_pureseqtm_installed()) {
  tally_tmhs(
    predict_topology(
      get_example_filename("1bhaA.fasta")
    )
  )
}
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())
uninstall_pureseqtm(folder_name = get_default_pureseqtm_folder())

Arguments

folder_name

name of the folder where the PureseqTM files are installed. The name of the PureseqTM binary file will be at [folder_name]/PureseqTM_Package

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Package 'pureseqtmr'

Help Index

Are the sequences transmembrance helices?

Description

Usage

Arguments

Value

Author(s)

Examples

Determine if these are all valid protein sequences

Description

Usage

Arguments

Value

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

Description

Usage

Arguments

Value

Author(s)

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

Description

Usage

Arguments

Value

Author(s)

Use Rcpp to calculate the distance to a TMH center

Description

Usage

Arguments

Value

Check one protein sequence

Description

Usage

Arguments

Details

Value

Examples

Check one or more protein sequences

Description

Usage

Arguments

Details

Value

Examples

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

Description

Usage

Arguments

Value

Author(s)

Examples

Check if the topology is valid.

Description

Usage

Arguments

Value

Author(s)

Examples

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

Description

Usage

Arguments

Value

Author(s)

Examples

Convert a TMHMM topology to a PureseqTM topology

Description

Usage

Arguments

Value

Author(s)

Examples

Count the number of TMHs in a topology

Description

Usage

Arguments

Examples

Create the five PureseqTM output files, by running PureseqTM.

Description