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Use ensembl database server instead of biomart

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This commit is contained in:
Elias Projahn 2023-11-08 12:15:26 +01:00
parent 948cb337db
commit 795fe99003
16 changed files with 373 additions and 452 deletions
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19
R/data.R
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@ -2,13 +2,26 @@
#'
#' @format A [data.table] with the following columns:
#' \describe{
#' \item{id}{Unique species ID}
#' \item{id}{Unique species ID, these are NCBI taxon IDs}
#' \item{name}{Human readable species name}
#' \item{scientific_name}{Scientific name of the species}
#' \item{table_name}{Table name within the Ensembl database}
#' \item{n_chromosomes}{Number of chromosomes}
#' \item{median_chromosome_length}{Median length of chromosomes}
#' }
"species"
#' Information on chromosomes for each included species.
#'
#' @format A [data.table] with the following columns:
#' \describe{
#' \item{species}{Species ID}
#' \item{id}{Chromosome ID, theses are Ensembl sequence IDs}
#' \item{name}{Chromosome name}
#' \item{length}{Length in base pairs}
#' }
"chromosomes"
#' Information on human genes within the Ensembl database.
#'
#' This includes only genes on the primary suggested assembly of the human
@ -18,7 +31,7 @@
#' \describe{
#' \item{id}{Ensembl gene ID}
#' \item{name}{The gene's HGNC name (if available)}
#' \item{chrosome}{The human chromosome the gene is located on}
#' \item{chromosome}{The human chromosome the gene is located on}
#' }
"genes"
@ -31,7 +44,7 @@
#' \describe{
#' \item{species}{Species ID}
#' \item{gene}{Gene ID}
#' \item{chromosome_name}{Chromosome name from the specified species}
#' \item{chromosome}{Chromosome ID}
#' \item{start_position}{Start position in base pairs}
#' \item{end_position}{End position in base pairs}
#' \item{distance}{Computed distance to nearest telomere}

11
R/plots.R
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@ -561,13 +561,14 @@ plot_scores_by_position <- function(ranking,
}
distance_data <- if (!is.null(chromosome_name)) {
chromosome_name_ <- chromosome_name
geposan::distances[
species == "hsapiens" &
chromosome_name == chromosome_name_
chromosome_id <- geposan::chromosomes[
species == "9606" & name == chromosome_name,
id
]
geposan::distances[species == "9606" & chromosome == chromosome_id]
} else {
geposan::distances[species == "hsapiens"]
geposan::distances[species == "9606"]
}
data <- merge(ranking, distance_data, by = "gene")