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input: Only connect to Ensembl if necessary

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This commit is contained in:
Elias Projahn 2021-10-11 10:17:58 +02:00
parent d87474e574
commit 48aa46c2c4
1 changed files with 15 additions and 6 deletions
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21
input.R
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@ -57,10 +57,17 @@ genes_suggested_tpe_old <- c(
"TSPAN9"
)
ensembl <- useEnsembl(
biomart = "ensembl",
version = 104
)
#' Shared accessor for the Ensembl API.
ensembl <- NULL
#' Get the ensembl accessor and initialize it if necessary.
get_ensembl <- function() {
if (is.null(ensembl)) {
ensembl <<- useEnsembl("ensembl", version = 104)
}
ensembl
}
#' Retrieve information on species.
#'
@ -71,7 +78,7 @@ ensembl <- useEnsembl(
#' - `replicative` Whether the species is likely to be aging replicatively.
retrieve_species <- function() {
# Ensembl datasets correspond to distinct species.
ensembl_datasets <- data.table(listDatasets(ensembl))
ensembl_datasets <- data.table(listDatasets(get_ensembl()))
# Filter out species ID and name from the result.
species <- ensembl_datasets[, .(
@ -92,7 +99,7 @@ retrieve_species <- function() {
retrieve_genes <- function() {
genes <- data.table(getBM(
attributes = c("ensembl_gene_id", "hgnc_symbol", "chromosome_name"),
mart = useDataset("hsapiens_gene_ensembl", mart = ensembl)
mart = useDataset("hsapiens_gene_ensembl", mart = get_ensembl())
))
genes[, .(
@ -116,6 +123,8 @@ retrieve_genes <- function() {
#' - `gene` Ensembl gene ID.
#' - `distance` Distance to nearest telomere in base pairs.
retrieve_distances <- function(species_ids, gene_ids) {
ensembl <- get_ensembl()
# Exclude the human from the species, in case it is present there.
species_ids <- species_ids[species_ids != "hsapiens"]