diff --git a/DESCRIPTION b/DESCRIPTION index 919c64e..1fc1c15 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -18,7 +18,7 @@ Encoding: UTF-8 LazyData: true LazyDataCompression: xz Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.0 +RoxygenNote: 7.2.3 Depends: R (>= 4.1) Imports: diff --git a/R/data.R b/R/data.R index 534425e..78f82c4 100644 --- a/R/data.R +++ b/R/data.R @@ -17,7 +17,7 @@ #' @format A [data.table] with the following columns: #' \describe{ #' \item{id}{Ensembl gene ID} -#' \item{name}{The gene's HGNC name} +#' \item{name}{The gene's HGNC name (if available)} #' \item{chrosome}{The human chromosome the gene is located on} #' } "genes" diff --git a/data/distances.rda b/data/distances.rda index 9763b49..deb1417 100644 Binary files a/data/distances.rda and b/data/distances.rda differ diff --git a/data/genes.rda b/data/genes.rda index f132a7d..d8a139e 100644 Binary files a/data/genes.rda and b/data/genes.rda differ diff --git a/data/species.rda b/data/species.rda index 5d0d7a5..3fd6e69 100644 Binary files a/data/species.rda and b/data/species.rda differ diff --git a/man/genes.Rd b/man/genes.Rd index 8b6671a..6d6c945 100644 --- a/man/genes.Rd +++ b/man/genes.Rd @@ -8,7 +8,7 @@ A \link{data.table} with the following columns: \describe{ \item{id}{Ensembl gene ID} -\item{name}{The gene's HGNC name} +\item{name}{The gene's HGNC name (if available)} \item{chrosome}{The human chromosome the gene is located on} } } diff --git a/scripts/chromosome_names.R b/scripts/chromosome_names.R index e516f49..8312716 100644 --- a/scripts/chromosome_names.R +++ b/scripts/chromosome_names.R @@ -19,7 +19,7 @@ get_species_ids <- function() { #' Get all chromosomes names for a species. get_species_chromosomes <- function(species_id) { - chromosomes <- unlist(ensembl_request( + unlist(ensembl_request( paste0("/info/assembly/", species_id) )$karyotype) } diff --git a/scripts/ensembl.R b/scripts/ensembl.R index ab052fc..814ab3f 100644 --- a/scripts/ensembl.R +++ b/scripts/ensembl.R @@ -3,7 +3,7 @@ library(data.table) rlog::log_info("Connecting to Ensembl API") # Object to access the Ensembl API. -ensembl <- biomaRt::useEnsembl("ensembl", version = 106) +ensembl <- biomaRt::useEnsembl("ensembl", version = 110) # Retrieve species information. @@ -42,69 +42,48 @@ valid_chromosome_names <- c( "17", "18", "19", - "20", "X", + "groupI", + "groupII", + "groupIII", + "groupIV", + "groupV", + "groupVI", + "groupVII", + "groupVIII", + "groupIX", + "groupX", + "groupXI", + "groupXII", + "groupXIII", + "groupXIV", + "groupXV", + "groupXVI", + "groupXVII", + "groupXVIII", + "groupXIX", + "groupXX", + "groupXXI", + "20", "Y", "21", - "4A", - "1A", "22", "23", "24", - "25LG1", - "25LG2", + "25", "26", "27", "28", - "LGE22", - "Z", - "25", "29", - "A1", - "A2", - "A3", - "B1", - "B2", - "B3", - "B4", - "C1", - "C2", - "D1", - "D2", - "D3", - "D4", - "E1", - "E2", - "E3", - "F1", - "F2", - "2A", - "2B", - "LG01", - "LG02", - "LG03", - "LG04", - "LG05", - "LG06", - "LG07", - "LG08", - "LG09", - "LG10", - "LG11", - "LG12", - "LG13", - "LG14", - "LG15", - "LG16", - "LG17", - "LG18", - "LG19", - "LG20", - "LG21", - "LG22", - "LG23", - "LG24", - "LG25", + "30", + "31", + "32", + "33", + "34", + "35", + "36", + "37", + "38", "I", "II", "III", @@ -128,53 +107,21 @@ valid_chromosome_names <- c( "XXII", "XXIII", "XXIV", + "7a", + "7b", + "Z", "W", - "30", - "31", - "32", - "33", - "34", - "35", - "36", - "37", - "38", + "a", + "b", + "c", + "d", + "f", + "g", + "h", "39", "40", - "2L", - "2R", - "3L", - "3R", - "LG1", - "LG2", - "LG3", - "LG4", - "LG5", - "LG6", - "LG7", - "LG8", - "LG9", - "LG26", - "LG27", - "LG28", - "LG29", - "LG30", "1a", - "7b", "22a", - "LGE22C19W28_E50C23", - "LGE64", - "7a", - "MIC_1", - "MIC_10", - "MIC_11", - "MIC_2", - "MIC_3", - "MIC_4", - "MIC_5", - "MIC_6", - "MIC_7", - "MIC_8", - "MIC_9", "sgr01", "sgr02", "sgr03", @@ -194,18 +141,95 @@ valid_chromosome_names <- c( "sgr17", "sgr18", "sgr19", + "LGE64", + "2A", + "2B", "X1", "X2", "X3", "X4", "X5", - "a", - "b", - "c", - "d", - "f", - "g", - "h", + "LG1", + "LG2", + "LG3", + "LG4", + "LG5", + "LG6", + "LG7", + "LG8", + "LG9", + "LG10", + "LG11", + "LG12", + "LG13", + "LG14", + "LG15", + "LG16", + "LG17", + "LG18", + "LG19", + "LG20", + "LG22", + "LG23", + "4A", + "1A", + "25LG1", + "25LG2", + "LGE22", + "LG21", + "A1", + "A2", + "A3", + "B1", + "B2", + "B3", + "B4", + "C1", + "C2", + "D1", + "D2", + "D3", + "D4", + "E1", + "E2", + "E3", + "F1", + "F2", + "LG34", + "LG35", + "LG24", + "LG25", + "LG26", + "LG27", + "LG28", + "LG29", + "LG30", + "MIC_1", + "MIC_10", + "MIC_11", + "MIC_2", + "MIC_3", + "MIC_4", + "MIC_5", + "MIC_6", + "MIC_7", + "MIC_8", + "MIC_9", + "2L", + "2R", + "3L", + "3R", + "LGE22C19W28_E50C23", + "LG01", + "LG02", + "LG03", + "LG04", + "LG05", + "LG06", + "LG07", + "LG08", + "LG09", + "LG7_11", "41", "42", "43", @@ -224,31 +248,7 @@ valid_chromosome_names <- c( "LG44F", "LG45M", "LG48F", - "LG49B", - "LG34", - "LG35", - "LG7_11", - "groupI", - "groupII", - "groupIII", - "groupIV", - "groupV", - "groupVI", - "groupVII", - "groupVIII", - "groupIX", - "groupX", - "groupXI", - "groupXII", - "groupXIII", - "groupXIV", - "groupXV", - "groupXVI", - "groupXVII", - "groupXVIII", - "groupXIX", - "groupXX", - "groupXXI" + "LG49B" ) #' Get all chromosome names for an Ensembl dataset.