Package 'ginmappeR'

Title: Gene Identifier Mapper
Description: Provides functionalities to translate gene or protein identifiers between state-of-art biological databases: CARD (<https://card.mcmaster.ca/>), NCBI Protein, Nucleotide and Gene (<https://www.ncbi.nlm.nih.gov/>), UniProt (<https://www.uniprot.org/>) and KEGG (<https://www.kegg.jp>). Also offers complementary functionality like NCBI identical proteins or UniProt similar genes clusters retrieval.
Authors: Fernando Sola [aut, cre] , Daniel Ayala [aut] , Marina Pulido [aut] , Rafael Ayala [aut] , Lorena López-Cerero [aut] , Inma Hernández [aut] , David Ruiz [aut]
Maintainer: Fernando Sola <[email protected]>
License: GPL-3 + file LICENSE
Version: 1.3.3
Built: 2024-12-03 03:13:55 UTC
Source: https://github.com/bioc/ginmappeR

Help Index

Change path to download CARD database

Description

Defines a new path to the folder where to download CARD database. By default, this path is the temporary folder tempdir().

Usage

changeCARDPath(path=tempdir())

Arguments

path

valid route to desired folder. Default value: tempdir()

Value

Updated path for CARD database to be downloaded.

Translates a CARD database ID to KEGG database

Description

Retrieves the ID translation of an specific instance of CARD database ID to the KEGG Genes database.

Usage

getCARD2KEGG(cardId, exhaustiveMapping = FALSE, detailedMapping = FALSE,
byIdenticalProteins = TRUE, bySimilarGenes = TRUE)

Arguments

cardId

valid CARD database ARO ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of KEGG IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

byIdenticalProteins

logical value (TRUE or FALSE) indicating to translate also through NCBI Identical Proteins. TRUE value could mean higher translation time and FALSE, fewer chances to translate the ID
bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as cardId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate CARD ID '3000938' to KEGG
getCARD2KEGG('3000938', byIdenticalProteins = FALSE, bySimilarGenes = FALSE)

# Translate CARD IDs '3000938' and '3002557' to KEGG
getCARD2KEGG(c('3000938', '3002557'))

# Get all possible translations of IDs '3000938', '3002511' with detailed origin
getCARD2KEGG(c('3000938', '3002511'), exhaustiveMapping = TRUE,
detailedMapping = TRUE)

Translates a CARD database ID to NCBI Gene database

Description

Retrieves the ID translation of an specific instance of CARD database ID to the NCBI Gene database.

Usage

getCARD2NCBIGene(cardId, exhaustiveMapping = FALSE)

Arguments

cardId

valid CARD database ARO ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as cardId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate CARD ID '3002525' to NCBI Gene
getCARD2NCBIGene('3002525')

# Translate CARD IDs '3002524' and '3002525' to NCBI Gene
getCARD2NCBIGene(c('3002524', '3002525'))

# Get all possible translations of IDs '3005061' and '3002524'
getCARD2NCBIGene(c('3005061', '3002524'), exhaustiveMapping = TRUE)

Translates a CARD database ID to NCBI Nucleotide database

Description

Retrieves the ID translation of an specific instance of CARD database ID to the NCBI Nucleotide database. Note that, due to the nature of NCBI Nucleotide database, a complete genome is often retrieved.

Usage

getCARD2NCBINucleotide(cardId)

Arguments

cardId

valid CARD database ARO ID or a vector of them

Value

A character vector of the same length as cardId.

Examples

# Translate CARD ID '3002535' to NCBI Nucleotide
getCARD2NCBINucleotide('3002535')

# Translate CARD ID 'ARO:3002535' to NCBI Nucleotide
getCARD2NCBINucleotide('ARO:3002535')

# Translate CARD IDs '3002535' and '3003988' to NCBI Nucleotide
getCARD2NCBINucleotide(c('3002535', '3003988'))

Translates a CARD database ID to NCBI Protein database

Description

Retrieves the ID translation of an specific instance of CARD database ID to the NCBI Protein database.

Usage

getCARD2NCBIProtein(cardId)

Arguments

cardId

valid CARD database ARO ID or a vector of them

Value

A character vector of the same length as cardId.

Examples

# Translate CARD ID '3002535' to NCBI Protein
getCARD2NCBIProtein('3002535')

# Translate CARD ID 'ARO:3002535' to NCBI Protein
getCARD2NCBIProtein('ARO:3002535')

# Translate CARD IDs '3002535' and '3003988' to NCBI Protein
getCARD2NCBIProtein(c('3002535', '3003988'))

Translates a CARD database ID to UniProt database

Description

Retrieves the ID translation of an specific instance of CARD database ID to the UniProt database.

Usage

getCARD2UniProt(cardId, exhaustiveMapping = FALSE, detailedMapping = FALSE)

Arguments

cardId

valid CARD database ARO ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of UniProt IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

Value

A character vector of the same length as cardId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate CARD ID '3002867' to UniProt
getCARD2UniProt('3002867')

# Translate CARD IDs '3002867' and '3002535' to UniProt
getCARD2UniProt(c('3002867', '3002535'))

# Get all possible translations of IDs '3002867', '3002535' with detailed origin
getCARD2UniProt(c('3002867', '3002535'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Prints CARD database version being used

Description

Prints the downloaded CARD version and release date.

Usage

getCARDVersion()

Value

Downloaded CARD database version.

Translates a KEGG database ID to CARD database

Description

Retrieves the ID translation of an specific instance of KEGG Genes database ID to the CARD database.

Usage

getKEGG2CARD(keggId, exhaustiveMapping = FALSE, detailedMapping = FALSE,
bySimilarGenes = TRUE)

Arguments

keggId

valid KEGG Genes database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of CARD IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as keggId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate KEGG ID 'ag:ACC85616' to CARD
getKEGG2CARD('ag:ACC85616')

# Translate KEGG IDs 'ag:ACC85616' and 'ag:CAJ47134' to CARD
getKEGG2CARD(c('ag:ACC85616', 'ag:CAJ47134'))

# Get all possible translations of IDs 'ag:ACC85616', 'ag:CAJ47134'
# with detailed origin
getKEGG2CARD(c('ag:ACC85616', 'ag:CAJ47134'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Translates a KEGG database ID to NCBI Gene database

Description

Retrieves the ID translation of an specific instance of KEGG Genes database ID to the NCBI Gene database.

Usage

getKEGG2NCBIGene(keggId, exhaustiveMapping = FALSE, detailedMapping = FALSE,
bySimilarGenes = TRUE)

Arguments

keggId

valid KEGG Genes database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of NCBI Gene IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as keggId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate KEGG ID 'aag:5579347' to NCBI Gene
getKEGG2NCBIGene('aag:5579347', detailedMapping = TRUE)

# Translate KEGG IDs 'aag:5579347' and 'abh:M3Q_2831' to NCBI Gene
getKEGG2NCBIGene(c('aag:5579347', 'abh:M3Q_2831'))

# Get all possible translations of IDs 'aag:5579347', 'abh:M3Q_2831' with
# detailed origin
getKEGG2NCBIGene(c('aag:5579347', 'abh:M3Q_2831'), exhaustiveMapping = TRUE,
detailedMapping = TRUE)

Translates a KEGG database ID to NCBI Nucleotide database

Description

Retrieves the ID translation of an specific instance of KEGG Genes database ID to the NCBI Nucleotide database. Note that, due to the nature of NCBI Nucleotide database, a complete genome is often retrieved.

Usage

getKEGG2NCBINucleotide(keggId, exhaustiveMapping = FALSE,
detailedMapping = FALSE, bySimilarGenes = TRUE)

Arguments

keggId

valid KEGG Genes database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of NCBI Nucleotide IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as keggId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate KEGG ID 'llo:LLO_2673' to NCBI Nucleotide
getKEGG2NCBINucleotide('llo:LLO_2673', bySimilarGenes = FALSE)

# Translate KEGG IDs 'llo:LLO_2673' and 'abh:M3Q_2831' to NCBI Nucleotide
getKEGG2NCBINucleotide(c('llo:LLO_2673', 'abh:M3Q_2831'))

# Get all possible translations of IDs 'aag:5579347', 'abh:M3Q_2831' with
# detailed origin
getKEGG2NCBINucleotide(c('aag:5579347', 'abh:M3Q_2831'),
exhaustiveMapping = TRUE, detailedMapping = TRUE)

Translates a KEGG database ID to NCBI Protein database

Description

Retrieves the ID translation of an specific instance of KEGG Genes database ID to the NCBI Protein database.

Usage

getKEGG2NCBIProtein(keggId, exhaustiveMapping = FALSE, detailedMapping = FALSE,
bySimilarGenes = TRUE)

Arguments

keggId

valid KEGG Genes database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of NCBI Protein IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as keggId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate KEGG ID 'llo:LLO_2673' to NCBI Protein
getKEGG2NCBIProtein('llo:LLO_2673')

# Translate KEGG IDs 'llo:LLO_2673' and 'abh:M3Q_2831' to NCBI Protein
getKEGG2NCBIProtein(c('llo:LLO_2673', 'abh:M3Q_2831'))

# Get all possible translations of IDs 'llo:LLO_2673', 'abh:M3Q_2831' with
# detailed origin
getKEGG2NCBIProtein(c('llo:LLO_2673', 'abh:M3Q_2831'),
exhaustiveMapping = TRUE, detailedMapping = TRUE)

Translates a KEGG Genes database ID to UniProt database

Description

Retrieves the ID translation of an specific instance of KEGG Genes database ID to the UniProt database.

Usage

getKEGG2UniProt(keggId, exhaustiveMapping = FALSE)

Arguments

keggId

valid KEGG Genes database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as keggId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate KEGG Genes ID 'llo:LLO_2673' to UniProt
getKEGG2UniProt('llo:LLO_2673')

# Translate KEGG IDs 'llo:LLO_2673' and 'abh:M3Q_2831' to NCBI UniProt
getKEGG2UniProt(c('llo:LLO_2673', 'abh:M3Q_2831'))

# Get all possible translations of IDs 'llo:LLO_2673', 'abh:M3Q_2831'
getKEGG2UniProt(c('llo:LLO_2673', 'abh:M3Q_2831'), exhaustiveMapping = TRUE)

Prints KEGG database version being used

Description

Prints the accessed KEGG version and its corresponding release date. It also prints the API version release date.

Usage

getKEGGVersion()

Value

KEGG database and API version.

Translates a NCBI Gene database ID to CARD database

Description

Retrieves the ID translation of an specific instance of NCBI Gene database ID to the CARD database.

Usage

getNCBIGene2CARD(ncbiId, exhaustiveMapping = FALSE)

Arguments

ncbiId

valid NCBI Gene database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as ncbiId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Gene ID '3510143' to CARD
getNCBIGene2CARD('3510143')

# Translate NCBI Gene IDs '3510143' and '29426913' to CARD
getNCBIGene2CARD(c('3510143', '29426913'))

# Get all possible translations of IDs '3510143' and '29426913'
getNCBIGene2CARD(c('3510143', '29426913'), exhaustiveMapping = TRUE)

Translates a NCBI Gene database ID to KEGG database

Description

Retrieves the ID translation of an specific instance of NCBI Gene database ID to the KEGG Genes database.

Usage

getNCBIGene2KEGG(ncbiId, exhaustiveMapping = FALSE, detailedMapping = FALSE,
byIdenticalProteins = TRUE, bySimilarGenes = TRUE)

Arguments

ncbiId

valid NCBI Gene database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of KEGG IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

byIdenticalProteins

logical value (TRUE or FALSE) indicating to translate also through NCBI Identical Proteins. TRUE value could mean higher translation time and FALSE, fewer chances to translate the ID
bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as ncbiId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Gene ID '76524190' to KEGG
getNCBIGene2KEGG('AFU38919', bySimilarGenes = FALSE, byIdenticalProteins = FALSE)

# Translate NCBI Gene IDs '76524190' and 'AFU38919' to KEGG
getNCBIGene2KEGG(c('76524190', 'AFU38919'))

# Get all possible translations of IDs '76524190' and 'AFU38919' with
# detailed origin
getNCBIGene2KEGG(c('76524190', 'AFU38919'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Translates a NCBI Gene database ID to NCBI Nucleotide database

Description

Retrieves the ID translation of an specific instance of NCBI Gene database ID to the NCBI Nucleotide database. Note that, due to the nature of NCBI Nucleotide database, a complete genome is often retrieved.

Usage

getNCBIGene2NCBINucleotide(id, exhaustiveMapping=FALSE)

Arguments

id

valid NCBI Gene database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as id. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Gene ID '76524190' to NCBI Nucleotide
getNCBIGene2NCBINucleotide('76524190')

# Translate NCBI Gene IDs '76524190' and '1272' to NCBI Nucleotide
getNCBIGene2NCBINucleotide(c('76524190', '1272'))

# Get all possible translations of IDs '76524190' and '1272'
getNCBIGene2NCBINucleotide(c('76524190', '1272'), exhaustiveMapping = TRUE)

Translates a NCBI Gene database ID to NCBI Protein database

Description

Retrieves the ID translation of an specific instance of NCBI Gene database ID to the NCBI Protein database.

Usage

getNCBIGene2NCBIProtein(id, exhaustiveMapping=FALSE)

Arguments

id

valid NCBI Gene database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as id. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Gene ID '76524190' to NCBI Protein
getNCBIGene2NCBIProtein('76524190')

# Translate NCBI Gene IDs '76524190' and '1272' to NCBI Protein
getNCBIGene2NCBIProtein(c('76524190', '1272'))

# Get all possible translations of IDs '76524190', '1272'
getNCBIGene2NCBIProtein(c('76524190', '1272'), exhaustiveMapping = TRUE)

Translates a NCBI Gene database ID to UniProt database

Description

Retrieves the ID translation of an specific instance of NCBI Gene database ID to the UniProt database.

Usage

getNCBIGene2UniProt(ncbiId, exhaustiveMapping = FALSE,
detailedMapping = FALSE, byIdenticalProteins = TRUE)

Arguments

ncbiId

valid NCBI Gene database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of UniProt IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

byIdenticalProteins

logical value (TRUE or FALSE) indicating to translate also through NCBI Identical Proteins. TRUE value could mean higher translation time and FALSE, fewer chances to translate the ID

Value

A character vector of the same length as ncbiId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Gene ID '76524190' to UniProt
getNCBIGene2UniProt('76524190')

# Translate NCBI Gene IDs '76524190' and '1272' to UniProt
getNCBIGene2UniProt(c('76524190', '1272'))

# Get all possible translations of IDs '76524190', '1272' with detailed origin
getNCBIGene2UniProt(c('76524190', '1272'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Search NCBI Identical Protein database by a given NCBI ID

Description

Retrieves identical NCBI proteins to that of a given ID.

Usage

getNCBIIdenticalProteins(ncbiId, format='ids')

Arguments

ncbiId

valid NCBI ID or a vector of them
format

return format of the response. Default value ids returns a vector of the identical proteins IDs; dataframe value returns a dataframe with different information about the found identical proteins

Value

Depending on parameter format, it will return a list of same legth as ncbiId with identical NCBI Protein IDs or with dataframes containing different information about the identical proteins found: Id, Source, Nucleotide.Accession, Start, Stop, Strand, Protein, Protein.Name, Organism, Strain and Assembly.

Examples

# Get IDs on identical proteins to the one with ID 'AHA80958'
getNCBIIdenticalProteins('AHA80958', format = 'ids')

# Get IDs on identical proteins to the ones with IDs 'AHA80958' and 'CAA76794'
getNCBIIdenticalProteins(c('AHA80958', 'CAA76794'), format = 'ids')

Translates a NCBI Nucleotide database ID to CARD database

Description

Retrieves the ID translation of an specific instance of NCBI Nucleotide database ID to the CARD database.

Usage

getNCBINucleotide2CARD(ncbiId, exhaustiveMapping = FALSE)

Arguments

ncbiId

valid NCBI Nucleotide database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as ncbiId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Nucleotide ID 'AY034138' to CARD
getNCBINucleotide2CARD('AY034138')

# Translate NCBI Nucleotide IDs 'AY034138' and 'X54723.1' to CARD
getNCBINucleotide2CARD(c('AY034138', 'X54723.1'))

# Get all possible translations of IDs 'AY034138', 'X54723.1'
getNCBINucleotide2CARD(c('AY034138', 'X54723.1'), exhaustiveMapping = TRUE)

Translates a NCBI Nucleotide database ID to KEGG database

Description

Retrieves the ID translation of an specific instance of NCBI Nucleotide database ID to the KEGG Genes database.

Usage

getNCBINucleotide2KEGG(ncbiId, exhaustiveMapping = FALSE,
detailedMapping = FALSE, byIdenticalProteins = TRUE, bySimilarGenes = TRUE)

Arguments

ncbiId

valid NCBI Nucleotide database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of KEGG IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

byIdenticalProteins

logical value (TRUE or FALSE) indicating to translate also through NCBI Identical Proteins. TRUE value could mean higher translation time and FALSE, fewer chances to translate the ID
bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as ncbiId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Nucleotide ID 'NC_013861.1' to KEGG
getNCBINucleotide2KEGG('NC_013861.1', bySimilarGenes = FALSE, byIdenticalProteins = FALSE)

# Translate NCBI Nucleotide IDs 'AY536519' and 'NC_013861.1' to KEGG
getNCBINucleotide2KEGG(c('AY536519', 'NC_013861.1'))

# Get all possible translations of IDs 'AY536519', 'NC_013861.1'
# with detailed origin
getNCBINucleotide2KEGG(c('AY536519', 'NC_013861.1'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Translates a NCBI Nucleotide database ID to NCBI Gene database

Description

Retrieves the ID translation of an specific instance of NCBI Nucleotide database ID to the NCBI Gene database.

Usage

getNCBINucleotide2NCBIGene(id, exhaustiveMapping=FALSE)

Arguments

id

valid NCBI Nucleotide database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as id. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Nucleotide ID 'Z21488' to NCBI Gene
getNCBINucleotide2NCBIGene('Z21488')

# Get all possible translations of ID 'Z21488'
getNCBINucleotide2NCBIGene(c('Z21488'), exhaustiveMapping = TRUE)

Translates a NCBI Nucleotide database ID to NCBI Protein database

Description

Retrieves the ID translation of an specific instance of NCBI Nucleotide database ID to the NCBI Protein database.

Usage

getNCBINucleotide2NCBIProtein(id, exhaustiveMapping=FALSE)

Arguments

id

valid NCBI Nucleotide database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as id. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Nucleotide ID 'AY536519' to NCBI Protein
getNCBINucleotide2NCBIProtein('AY536519')

# Translate NCBI Nucleotide IDs 'AY536519' and 'X54723.1' to NCBI Protein
getNCBINucleotide2NCBIProtein(c('AY536519', 'X54723.1'))

# Get all possible translations of IDs 'AY536519', 'X54723.1'
getNCBINucleotide2NCBIProtein(c('AY536519', 'X54723.1'),
exhaustiveMapping = TRUE)

Translates a NCBI Nucleotide database ID to UniProt database

Description

Retrieves the ID translation of an specific instance of NCBI Nucleotide database ID to the UniProt database.

Usage

getNCBINucleotide2UniProt(ncbiId, exhaustiveMapping = FALSE,
detailedMapping = FALSE, byIdenticalProteins = TRUE)

Arguments

ncbiId

valid NCBI Nucleotide database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of UniProt IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

byIdenticalProteins

logical value (TRUE or FALSE) indicating to translate also through NCBI Identical Proteins. TRUE value could mean higher translation time and FALSE, fewer chances to translate the ID

Value

A character vector of the same length as ncbiId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Nucleotide ID 'AY536519' to UniProt
getNCBINucleotide2UniProt('AY536519')

# Translate NCBI Nucleotide IDs 'AY536519' and 'X54723.1' to UniProt
getNCBINucleotide2UniProt(c('AY536519', 'X54723.1'))

# Get all possible translations of IDs 'AY536519', 'X54723.1'
# with detailed origin
getNCBINucleotide2UniProt(c('AY536519', 'X54723.1'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Translates a NCBI Protein database ID to CARD database

Description

Retrieves the ID translation of an specific instance of NCBI Protein database ID to the CARD database.

Usage

getNCBIProtein2CARD(ncbiId, exhaustiveMapping = FALSE)

Arguments

ncbiId

valid NCBI Protein database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as ncbiId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Protein ID 'AAK64581' to CARD
getNCBIProtein2CARD('AAK64581')

# Translate NCBI Protein IDs 'AAK64581' and 'WP_010896559.1' to CARD
getNCBIProtein2CARD(c('AAK64581', 'WP_010896559.1'))

# Get all possible translations of IDs 'AAK64581', 'WP_010896559.1'
getNCBIProtein2CARD(c('AAK64581', 'WP_010896559.1'), exhaustiveMapping = TRUE)

Translates a NCBI Protein database ID to KEGG database

Description

Retrieves the ID translation of an specific instance of NCBI Protein database ID to the KEGG Genes database.

Usage

getNCBIProtein2KEGG(ncbiId, exhaustiveMapping = FALSE, detailedMapping = FALSE,
byIdenticalProteins = TRUE, bySimilarGenes = TRUE)

Arguments

ncbiId

valid NCBI Protein database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of KEGG IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

byIdenticalProteins

logical value (TRUE or FALSE) indicating to translate also through NCBI Identical Proteins. TRUE value could mean higher translation time and FALSE, fewer chances to translate the ID
bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as ncbiId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Protein ID 'AFU38919' to KEGG
getNCBIProtein2KEGG('AFU38919', exhaustiveMapping = FALSE,
detailedMapping = FALSE, byIdenticalProteins = FALSE, bySimilarGenes = FALSE)

# Translate NCBI Protein IDs 'AFU38919' and 'WP_010896559.1' to KEGG
getNCBIProtein2KEGG(c('AFU38919', 'WP_010896559.1'),
byIdenticalProteins = FALSE)

# Get all possible translations of ID 'AFU38919', 'WP_010896559.1'
# with detailed origin
getNCBIProtein2KEGG(c('AFU38919', 'WP_010896559.1'), exhaustiveMapping = TRUE,
detailedMapping = TRUE)

Translates a NCBI Protein database ID to NCBI Gene database

Description

Retrieves the ID translation of an specific instance of NCBI Protein database ID to the NCBI Gene database.

Usage

getNCBIProtein2NCBIGene(id, exhaustiveMapping=FALSE)

Arguments

id

valid NCBI Protein database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as id. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Protein ID 'CAA79696' to NCBI Gene
getNCBIProtein2NCBIGene('CAA79696')

# Translate NCBI Protein IDs 'CAA79696' and 'WP_001082319' to NCBI Gene
getNCBIProtein2NCBIGene(c('CAA79696', 'WP_001082319'))

# Get all possible translations of IDs 'CAA79696', 'WP_001082319'
getNCBIProtein2NCBIGene(c('CAA79696', 'WP_001082319'), exhaustiveMapping=TRUE)

Translates a NCBI Protein database ID to NCBI Nucleotide database

Description

Retrieves the ID translation of an specific instance of NCBI Protein database ID to the NCBI Nucleotide database. Note that, due to the nature of NCBI Nucleotide database, a complete genome is often retrieved.

Usage

getNCBIProtein2NCBINucleotide(id, exhaustiveMapping=FALSE)

Arguments

id

valid NCBI Protein database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.

Value

A character vector of the same length as id. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Protein ID 'AAS48620' to NCBI Nucleotide
getNCBIProtein2NCBINucleotide('AAS48620')

# Translate NCBI Protein IDs 'AAS48620' and 'CAA38525' to NCBI Nucleotide
getNCBIProtein2NCBINucleotide(c('AAS48620', 'CAA38525'))

# Get all possible translations of IDs 'AAS48620', 'CAA38525'
getNCBIProtein2NCBINucleotide(c('AAS48620', 'CAA38525'), exhaustiveMapping=TRUE)

Translates a NCBI Protein database ID to UniProt database

Description

Retrieves the ID translation of an specific instance of NCBI Protein database ID to the UniProt database.

Usage

getNCBIProtein2UniProt(ncbiId, exhaustiveMapping = FALSE,
detailedMapping = FALSE, byIdenticalProteins = TRUE)

Arguments

ncbiId

valid NCBI Protein database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of UniProt IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

byIdenticalProteins

logical value (TRUE or FALSE) indicating to translate also through NCBI Identical Proteins. TRUE value could mean higher translation time and FALSE, fewer chances to translate the ID

Value

A character vector of the same length as ncbiId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate NCBI Protein ID 'WP_010896559.1' to UniProt
getNCBIProtein2UniProt('WP_010896559.1')

# Translate NCBI Protein IDs 'AAS48620' and 'WP_010896559' to UniProt
getNCBIProtein2UniProt(c('AAS48620', 'WP_010896559'))

# Get all possible translations of IDs 'AAS48620', 'WP_010896559'
# with detailed origin
getNCBIProtein2UniProt(c('AAS48620', 'WP_010896559'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Prints NCBI databases versions being used

Description

Prints the build version and release date of the Protein, Gene, Nucleotide and Identical Proteins NCBI databases.

Usage

getNCBIVersion()

Value

NCBI databases versions.

Translates an UniProt database ID to CARD database

Description

Retrieves the ID translation of an specific instance of UniProt database ID to the CARD database.

Usage

getUniProt2CARD(upId, exhaustiveMapping = FALSE, detailedMapping = FALSE,
bySimilarGenes = TRUE)

Arguments

upId

valid UniProt database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of CARD IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as upId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate UniProt ID 'A0A1S7BGS4' to CARD
getUniProt2CARD('A0A1S7BGS4')

# Translate UniProt IDs 'A0A1S7BGS4' and 'A0A6H2TXZ6' to CARD
getUniProt2CARD(c('A0A1S7BGS4', 'A0A6H2TXZ6'))

# Get all possible translations of IDs 'A0A1S7BGS4', 'A0A6H2TXZ6'
# with detailed origin
getUniProt2CARD(c('A0A1S7BGS4', 'A0A6H2TXZ6'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Translates an UniProt database ID to KEGG database

Description

Retrieves the ID translation of an specific instance of UniProt database ID to the KEGG Genes database.

Usage

getUniProt2KEGG(upId, exhaustiveMapping = FALSE, bySimilarGenes = TRUE,
detailedMapping = FALSE)

Arguments

upId

valid UniProt database ID or a vector of them.
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of KEGG IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

Value

A character vector of the same length as upId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate UniProt ID 'G9JVE6' to KEGG
getUniProt2KEGG('G9JVE6')

# Translate UniProt IDs 'A0A1S7BGS4' and 'G9JVE6' to KEGG
getUniProt2KEGG(c('A0A1S7BGS4', 'G9JVE6'))

# Get all possible translations of ID 'A0A2R4PHC7' with detailed origin
getUniProt2KEGG(c('test_id', 'A0A2R4PHC7'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Translates an UniProt database ID to NCBI Gene database

Description

Retrieves the ID translation of an specific instance of UniProt database ID to the NCBI Gene database.

Usage

getUniProt2NCBIGene(upId, exhaustiveMapping = FALSE, detailedMapping = FALSE,
bySimilarGenes = TRUE)

Arguments

upId

valid UniProt database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of NCBI Gene IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as upId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate UniProt ID 'G9JVE6' to NCBI Gene
getUniProt2NCBIGene('G9JVE6')

# Translate UniProt IDs 'A0SNL9' and 'G9JVE6' to NCBI Gene
getUniProt2NCBIGene(c('A0SNL9', 'G9JVE6'))

# Get all possible translations of IDs 'A0SNL9', 'G9JVE6' with detailed origin
getUniProt2NCBIGene(c('A0SNL9', 'G9JVE6'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Translates an UniProt database ID to NCBI Nucleotide database

Description

Retrieves the ID translation of an specific instance of UniProt database ID to the NCBI Nucleotide database. Note that, due to the nature of NCBI Nucleotide database, a complete genome is often retrieved.

Usage

getUniProt2NCBINucleotide(upId, exhaustiveMapping = FALSE,
detailedMapping = FALSE, bySimilarGenes = TRUE)

Arguments

upId

valid UniProt database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of NCBI Nucleotide IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as upId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate UniProt ID 'G9JVE6' to NCBI Nucleotide
getUniProt2NCBINucleotide('G9JVE6')

# Translate UniProt IDs 'A0SNL9' and 'G9JVE6' to NCBI Nucleotide
getUniProt2NCBINucleotide(c('A0SNL9', 'G9JVE6'))

# Get all possible translations of IDs 'A0SNL9', 'G9JVE6' with detailed origin
getUniProt2NCBINucleotide(c('A0SNL9', 'G9JVE6'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Translates an UniProt database ID to NCBI Protein database

Description

Retrieves the ID translation of an specific instance of UniProt database ID to the NCBI Protein database.

Usage

getUniProt2NCBIProtein(upId, exhaustiveMapping = FALSE, detailedMapping = FALSE,
bySimilarGenes = TRUE)

Arguments

upId

valid UniProt database ID or a vector of them
exhaustiveMapping

logical value (TRUE or FALSE) indicating to retrieve all possible translations or only the first and fastest one.
detailedMapping

logical value (TRUE or FALSE) indicating to return a vector of NCBI Protein IDs if FALSE, or a named vector if TRUE. This named vector details the origin of the translated IDs, dividing them in DT, if it is a Direct Translation, or 1.0, 0.9 or 0.5, if it has been retrieved through any of the identical gene clusters.

bySimilarGenes

logical value (TRUE or FALSE) indicating to translate also through similar UniProt genes (100%, 90% or 50% of identity). Using TRUE value may take a long time, only advised if there is not a direct translation possible.

Value

A character vector of the same length as upId. If parameter exhaustiveMapping is TRUE, it will return a list instead of a character vector to avoid mixing the identifiers.

Examples

# Translate UniProt ID 'G9JVE6' to NCBI Protein
getUniProt2NCBIProtein('G9JVE6')

# Translate UniProt IDs 'A0SNL9' and 'G9JVE6' to NCBI Protein
getUniProt2NCBIProtein(c('A0SNL9', 'G9JVE6'))

# Get all possible translations of IDs 'A0SNL9', 'G9JVE6' with detailed origin
getUniProt2NCBIProtein(c('A0SNL9', 'G9JVE6'), detailedMapping = TRUE,
exhaustiveMapping = TRUE)

Get similar UniProt genes by a given identity percentage

Description

Retrieves the cluster of genes with a certain percentage of identity where a given UniProt gene belongs.

Usage

getUniProtSimilarGenes(upId, clusterIdentity = '1.0', clusterNames = FALSE)

Arguments

upId

valid UniProt ID or a vector of them
clusterIdentity

identity of the cluster to be retrieved. Default value 1.0 returns the 100% identical genes cluster, values 0.9 and 0.5, the 90% and 50% identical genes clusters, respectively
clusterNames

logical value (TRUE or FALSE) indicating if cluster names are retrieved

Value

A list of the same length as upId. If parameter clusterNames is TRUE it will return a named list.

Examples

# Get UniProt IDs of 50% identical genes of UniProt gene 'G0L217'
getUniProtSimilarGenes('G0L217', clusterIdentity = '0.5')

# Get UniProt IDs of 50% identical genes of UniProt genes 'G0L217' and 'A0SNL9'
getUniProtSimilarGenes(c('G0L217', 'A0SNL9'), clusterIdentity = '0.5')

Prints UniProt database version being used

Description

Prints the accessed UniProt version and its corresponding release date.

Usage

getUniProtVersion()

Value

UniProt database version.

Downloads the most up-to-date version of CARD database

Description

Cleans previous CARD database versions if there were, and downloads its latest version.

Usage

updateCARDDataBase()

Value

Downloaded CARD database.