Predict Transmembrane Protein Topology

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Documentation for package ‘pureseqtmr’ version 1.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

are_tmhs	Are the sequences transmembrance helices?
are_valid_protein_sequences	Determine if these are all valid protein sequences
calc_distance_to_tmh_center_from_topology	Calculate the the distance for each amino acid to the center of the TMH
calc_distance_to_tmh_center_from_topology_str	Calculate the the distance for each amino acid to the center of the TMH
calc_distance_to_tmh_center_from_topology_str_cpp_stl	Use Rcpp to calculate the distance to a TMH center
check_protein_sequence	Check one protein sequence
check_protein_sequences	Check one or more protein sequences
check_pureseqtm_installation	Checks the installation of PureseqTM. Throws a helpful error message if incomplete, else does nothing
check_topology	Check if the topology is valid.
check_topology_str	Check if the topology string is valid. Will stop if not.
convert_tmhmm_to_pureseqtm_topology	Convert a TMHMM topology to a PureseqTM topology
count_n_tmhs	Count the number of TMHs in a topology
create_pureseqtm_files	Create the five PureseqTM output files, by running PureseqTM.
create_pureseqtm_proteome_file	Create the output file of a PureseqTM proteome run
default_params_doc	This function does nothing. It is intended to inherit is parameters' documentation.
get_default_pureseqtm_folder	Get the path to the folder where this package installs PureseqTM by default
get_example_filename	Get the full path to a PureseqTM example file.
get_example_filenames	Get the full path to all PureseqTM example files
get_pureseqtm_url	Get the URL of the PureseqTM source code
get_pureseqtm_version	Get the PureseqTM version
install_pureseqtm	Install PureseqTM to a local folder
is_on_appveyor	Determines if the environment is AppVeyor
is_on_ci	Determines if the environment is a continuous integration service
is_on_github_actions	Determines if the environment is GitHub Actions
is_on_travis	Determines if the environment is Travis CI
is_protein_name_line	Is the line of text the name of a protein, as used within a FASTA filename?
is_pureseqtm_installed	Measure if PureseqTM is installed locally
is_tmh	Determine if the protein sequence contains at least one transmembrane helix.
is_topology_line	Is the line of text the topology, as used within a FASTA filename?
is_valid_protein_sequence	Determine if this a valid protein sequence
load_fasta_file_as_tibble	Parse a FASTA file to a table with a 'name' and 'sequence' column
load_fasta_file_as_tibble_cpp	Parse a FASTA file to a table with a 'name' and 'sequence' column
load_fasta_file_as_tibble_cpp_raw	Use Rcpp to load a FASTA file
load_fasta_file_as_tibble_r	Parse a FASTA file to a table with a 'name' and 'sequence' column
load_topology_file_as_tibble	Parse a topology ('.topo') file to a table with a 'name' and 'topology' column
mock_predict_topologies_from_sequences	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.
mock_predict_topology	Do a mock prediction of the topology of proteins
parse_pureseqtm_proteome_text	Parse the output of a call to 'PureseqTM_proteome.sh'
plot_topology	Plot the topology
predict_topologies_from_sequences	Run PureseqTM directy on a protein sequence
predict_topology	Predict the topology of proteins from file
predict_topology_from_sequence	Run PureseqTM directy on a protein sequence
pureseqtmr	pureseqtmr: estimate the topoplogy of membrane proteins
pureseqtmr_report	Create a pureseqtmr report, to be used when reporting bugs
run_pureseqtm_proteome	Run PureseqTM on a proteome
save_tibble_as_fasta_file	Save the first two columns of a tibble as a FASTA file
tally_tmhs	Count the number of transmembrane helices in a topology
uninstall_pureseqtm	Uninstall PureseqTM