R/mi_get_ID_attr.R

In MantaID: A Machine-Learning Based Tool to Automate the Identification of Biological Database IDs

#' Get ID attributes from the `Biomart` database.
#' @param dataset Datasets of the selected BioMart database.
#' @param mirror Specify an Ensembl mirror to connect to.
#' @param biomart BioMart database name you want to connect to.Use `biomaRt::listEnsembl` to retrieve the possible database names.
#' @importFrom dplyr filter
#' @importFrom stringr str_length
#' @importFrom biomaRt useEnsembl listAttributes
#' @importFrom magrittr %>%
#' @return A dataframe.
#' @export

#Select the Ensemble dataset of eligible human genes in the BioMart database.
mi_get_ID_attr <- function(biomart = "genes", dataset = "hsapiens_gene_ensembl", mirror = "asia") {
  #Connect to selected BioMart databases and datasets hosted by Ensemble.
  ensemb_hm_dset <- useEnsembl(biomart = biomart, dataset = dataset, mirror = mirror, verbose = TRUE)
  #Filter attributes from the description column that contain ID or name but not end, start, description, probe, version, content, Aberrant,Source,Strain ,Chromosome, BioGrid, evidence and are less than 18 characters long.
  attributes <- listAttributes(ensemb_hm_dset) %>%
    filter(grepl(.[["description"]], pattern = "([iI][dD])|(name)", ignore.case = TRUE)) %>%
    filter(!grepl(.[["description"]], pattern = "(end)|(start)|(description)|(probe)|(version)|(content)|(Aberrant)|(Source)|(Strain)|(Chromosome)|(BioGRID)|(evidence)", ignore.case = TRUE)) %>%
    filter(!grepl(.[["name"]], pattern = "(homolog)|(paralog)", ignore.case = TRUE))
}