From de65de3bfe0b826d0016d1d4151961e4ba170f8c Mon Sep 17 00:00:00 2001 From: Moosa Rezwani Date: Tue, 31 Dec 2024 07:04:47 +0100 Subject: [PATCH] change uniprot location function names to comply with naming schema --- NAMESPACE | 4 ++-- R/uniprot_coordinates.R | 18 +++++++++--------- _pkgdown.yml | 2 +- man/rba_uniprot_coordinates.Rd | 6 +++--- man/rba_uniprot_coordinates_location.Rd | 6 +++--- ...rba_uniprot_coordinates_location_genome.Rd} | 12 ++++++------ ...ba_uniprot_coordinates_location_protein.Rd} | 14 +++++++------- man/rba_uniprot_coordinates_search.Rd | 4 ++-- 8 files changed, 33 insertions(+), 33 deletions(-) rename man/{rba_uniprot_genome_coordinates_sequence.Rd => rba_uniprot_coordinates_location_genome.Rd} (90%) rename man/{rba_uniprot_coordinates_sequence.Rd => rba_uniprot_coordinates_location_protein.Rd} (86%) diff --git a/NAMESPACE b/NAMESPACE index cd2e8c7..922e3d9 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -84,15 +84,15 @@ export(rba_uniprot_antigens) export(rba_uniprot_antigens_search) export(rba_uniprot_coordinates) export(rba_uniprot_coordinates_location) +export(rba_uniprot_coordinates_location_genome) +export(rba_uniprot_coordinates_location_protein) export(rba_uniprot_coordinates_search) -export(rba_uniprot_coordinates_sequence) export(rba_uniprot_epitope) export(rba_uniprot_epitope_search) export(rba_uniprot_features) export(rba_uniprot_features_search) export(rba_uniprot_genecentric) export(rba_uniprot_genecentric_search) -export(rba_uniprot_genome_coordinates_sequence) export(rba_uniprot_mutagenesis) export(rba_uniprot_mutagenesis_search) export(rba_uniprot_proteins) diff --git a/R/uniprot_coordinates.R b/R/uniprot_coordinates.R index 2b4f79a..05f0e57 100644 --- a/R/uniprot_coordinates.R +++ b/R/uniprot_coordinates.R @@ -185,20 +185,20 @@ rba_uniprot_coordinates_search <- function(accession = NULL, #' #' @examples #' \donttest{ -#' rba_uniprot_coordinates_sequence(accession = "P25942", p_position = 1) +#' rba_uniprot_coordinates_location_protein(accession = "P25942", p_position = 1) #' } #' \donttest{ -#' rba_uniprot_coordinates_sequence(accession = "P25942", +#' rba_uniprot_coordinates_location_protein(accession = "P25942", #' p_start = 1, p_end = 277) #' } #' #' @family "UniProt - Coordinates" #' @export -rba_uniprot_coordinates_sequence <- function(accession, - p_position = NULL, - p_start = NULL, - p_end = NULL, - ...) { +rba_uniprot_coordinates_location_protein <- function(accession, + p_position = NULL, + p_start = NULL, + p_end = NULL, + ...) { ## Load Global Options .rba_ext_args(...) ## Check User-input Arguments @@ -489,13 +489,13 @@ rba_uniprot_coordinates_location <- function(taxid, #' #' @examples #' \donttest{ -#' rba_uniprot_genome_coordinates_sequence( +#' rba_uniprot_coordinates_location_genome( #' taxid = 9606, chromosome = 11, g_position = 36573305) #' } #' #' @family "UniProt - Coordinates" #' @export -rba_uniprot_genome_coordinates_sequence <- function(taxid, +rba_uniprot_coordinates_location_genome <- function(taxid, chromosome, g_position = NULL, g_start = NULL, diff --git a/_pkgdown.yml b/_pkgdown.yml index 871f7e9..eb00474 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -201,5 +201,5 @@ reference: - starts_with("rba_uniprot_coordinates") - subtitle: "Uniparc" contents: - - starts_with("rba_uniprot_coordinates") + - starts_with("rba_uniprot") diff --git a/man/rba_uniprot_coordinates.Rd b/man/rba_uniprot_coordinates.Rd index 90d6f6a..b6d6b9d 100644 --- a/man/rba_uniprot_coordinates.Rd +++ b/man/rba_uniprot_coordinates.Rd @@ -69,8 +69,8 @@ rba_uniprot_coordinates(db_type = "HGNC", db_id = "CD40") \seealso{ Other "UniProt - Coordinates": \code{\link{rba_uniprot_coordinates_location}()}, -\code{\link{rba_uniprot_coordinates_search}()}, -\code{\link{rba_uniprot_coordinates_sequence}()}, -\code{\link{rba_uniprot_genome_coordinates_sequence}()} +\code{\link{rba_uniprot_coordinates_location_genome}()}, +\code{\link{rba_uniprot_coordinates_location_protein}()}, +\code{\link{rba_uniprot_coordinates_search}()} } \concept{"UniProt - Coordinates"} diff --git a/man/rba_uniprot_coordinates_location.Rd b/man/rba_uniprot_coordinates_location.Rd index 77d6fe8..68a0792 100644 --- a/man/rba_uniprot_coordinates_location.Rd +++ b/man/rba_uniprot_coordinates_location.Rd @@ -76,8 +76,8 @@ rba_uniprot_coordinates_location(taxid = 9606, \seealso{ Other "UniProt - Coordinates": \code{\link{rba_uniprot_coordinates}()}, -\code{\link{rba_uniprot_coordinates_search}()}, -\code{\link{rba_uniprot_coordinates_sequence}()}, -\code{\link{rba_uniprot_genome_coordinates_sequence}()} +\code{\link{rba_uniprot_coordinates_location_genome}()}, +\code{\link{rba_uniprot_coordinates_location_protein}()}, +\code{\link{rba_uniprot_coordinates_search}()} } \concept{"UniProt - Coordinates"} diff --git a/man/rba_uniprot_genome_coordinates_sequence.Rd b/man/rba_uniprot_coordinates_location_genome.Rd similarity index 90% rename from man/rba_uniprot_genome_coordinates_sequence.Rd rename to man/rba_uniprot_coordinates_location_genome.Rd index 297641a..922e6d4 100644 --- a/man/rba_uniprot_genome_coordinates_sequence.Rd +++ b/man/rba_uniprot_coordinates_location_genome.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/uniprot_coordinates.R -\name{rba_uniprot_genome_coordinates_sequence} -\alias{rba_uniprot_genome_coordinates_sequence} +\name{rba_uniprot_coordinates_location_genome} +\alias{rba_uniprot_coordinates_location_genome} \title{Get Genome coordinate by Gene Sequence position} \usage{ -rba_uniprot_genome_coordinates_sequence( +rba_uniprot_coordinates_location_genome( taxid, chromosome, g_position = NULL, @@ -54,7 +54,7 @@ For more information about how UniProt imports and calculates genomic \examples{ \donttest{ - rba_uniprot_genome_coordinates_sequence( + rba_uniprot_coordinates_location_genome( taxid = 9606, chromosome = 11, g_position = 36573305) } @@ -79,7 +79,7 @@ For more information about how UniProt imports and calculates genomic Other "UniProt - Coordinates": \code{\link{rba_uniprot_coordinates}()}, \code{\link{rba_uniprot_coordinates_location}()}, -\code{\link{rba_uniprot_coordinates_search}()}, -\code{\link{rba_uniprot_coordinates_sequence}()} +\code{\link{rba_uniprot_coordinates_location_protein}()}, +\code{\link{rba_uniprot_coordinates_search}()} } \concept{"UniProt - Coordinates"} diff --git a/man/rba_uniprot_coordinates_sequence.Rd b/man/rba_uniprot_coordinates_location_protein.Rd similarity index 86% rename from man/rba_uniprot_coordinates_sequence.Rd rename to man/rba_uniprot_coordinates_location_protein.Rd index a03a585..20bb9b9 100644 --- a/man/rba_uniprot_coordinates_sequence.Rd +++ b/man/rba_uniprot_coordinates_location_protein.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/uniprot_coordinates.R -\name{rba_uniprot_coordinates_sequence} -\alias{rba_uniprot_coordinates_sequence} +\name{rba_uniprot_coordinates_location_protein} +\alias{rba_uniprot_coordinates_location_protein} \title{Get Genome coordinate by Protein Sequence position} \usage{ -rba_uniprot_coordinates_sequence( +rba_uniprot_coordinates_location_protein( accession, p_position = NULL, p_start = NULL, @@ -51,10 +51,10 @@ For more information about how UniProt imports and calculates genomic \examples{ \donttest{ -rba_uniprot_coordinates_sequence(accession = "P25942", p_position = 1) +rba_uniprot_coordinates_location_protein(accession = "P25942", p_position = 1) } \donttest{ -rba_uniprot_coordinates_sequence(accession = "P25942", +rba_uniprot_coordinates_location_protein(accession = "P25942", p_start = 1, p_end = 277) } @@ -79,7 +79,7 @@ rba_uniprot_coordinates_sequence(accession = "P25942", Other "UniProt - Coordinates": \code{\link{rba_uniprot_coordinates}()}, \code{\link{rba_uniprot_coordinates_location}()}, -\code{\link{rba_uniprot_coordinates_search}()}, -\code{\link{rba_uniprot_genome_coordinates_sequence}()} +\code{\link{rba_uniprot_coordinates_location_genome}()}, +\code{\link{rba_uniprot_coordinates_search}()} } \concept{"UniProt - Coordinates"} diff --git a/man/rba_uniprot_coordinates_search.Rd b/man/rba_uniprot_coordinates_search.Rd index 158aea5..9f31e3b 100644 --- a/man/rba_uniprot_coordinates_search.Rd +++ b/man/rba_uniprot_coordinates_search.Rd @@ -92,7 +92,7 @@ rba_uniprot_coordinates_search(taxid = 9606, chromosome = "y") Other "UniProt - Coordinates": \code{\link{rba_uniprot_coordinates}()}, \code{\link{rba_uniprot_coordinates_location}()}, -\code{\link{rba_uniprot_coordinates_sequence}()}, -\code{\link{rba_uniprot_genome_coordinates_sequence}()} +\code{\link{rba_uniprot_coordinates_location_genome}()}, +\code{\link{rba_uniprot_coordinates_location_protein}()} } \concept{"UniProt - Coordinates"}