R/ensembl_db_retrieval.R

In EliLillyCo/surfaltr: Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

#' Retrieve Transcript Information from Ensembl for all Primary Transcripts
#'
#' This function retrieves all the primary transcripts in the given organism
#' and their corresponding gene names, APPRIS annotations, and UniProt IDs.
#'
#' @usage ensembl_db_retrieval(organism)
#' @param organism String indicating if mouse or human transcripts should be
#' retrieved
#' @importFrom biomaRt useEnsembl
#' @importFrom biomaRt getBM
#' @importFrom httr set_config
#' @importFrom httr config
#' @return A data frame containing the gene names, transcript IDs, APPRIS
#' annotations, UniProt Swissprot IDs, UniProt Swissprot isoform IDs, and
#' UniProt TREMBL IDs for all the primary transcripts in an organism.

ensembl_db_retrieval <- function(organism) {
    if (organism == "human") {
        httr::set_config(config(ssl_verifypeer = 0L))
        ensembl <- biomaRt::useEnsembl(biomart = "genes", 
        dataset = "hsapiens_gene_ensembl", mirror = "useast")
        humandb <- biomaRt::getBM(
            attributes = c(
                "external_gene_name", "ensembl_gene_id",
                "ensembl_transcript_id", "transcript_appris",
                "uniprotswissprot", "uniprotsptrembl", "uniprot_isoform"
            ),
            mart = ensembl
        )
        princ <- humandb[which(humandb$transcript_appris == "principal1" |
            humandb$transcript_appris == "principal2" |
            humandb$transcript_appris == "principal3" |
            humandb$transcript_appris == "principal4" |
            humandb$transcript_appris == "principal5"), ]
    }

    if (organism == "mouse") {
        httr::set_config(httr::config(ssl_verifypeer = 0L))
        ensembl <- biomaRt::useEnsembl(biomart = "genes", 
        dataset = "mmusculus_gene_ensembl")
        mousedb <- biomaRt::getBM(
            attributes = c(
                "external_gene_name", "ensembl_gene_id",
                "ensembl_transcript_id", "transcript_appris",
                "uniprotswissprot", "uniprotsptrembl", "uniprot_isoform"
            ),
            mart = ensembl
        )
        princ <- mousedb[which(mousedb$transcript_appris == "principal1" |
            mousedb$transcript_appris == "principal2" |
            mousedb$transcript_appris == "principal3" |
            mousedb$transcript_appris == "principal4" |
            mousedb$transcript_appris == "principal5"), ]
    }
    return(princ)
}