R/merge_trans.R

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

#' Associate Inputted Transcripts with Corresponding Primary Transcripts
#'
#' This function matches each inputted transcript with its corresponding
#' primary transcripts and returns a data frame containing the gene name,
#' transcript ID and APPRIS annotation for each.
#'
#' @usage merge_trans(princ, final_trans, if_aa)
#' @param princ Data frame containing all primary transcripts and relevant
#' gene information for an organism
#' @param final_trans Data frame containing cleaned and formatted input data
#' @param if_aa Boolean value indicating if the input file contains
#' amino acid sequences with TRUE indicating that sequences are present and
#' FALSE indicating that only IDs are present
#' @return A data frame containing gene names, transcript IDs, and APPRIS
#' annotations for all inputted data and its corresponding primary transcripts.
#' If sequences were provided, the data frame will also contain
#' the amino acid sequences. If only IDs were provided, the data frame will
#' also contain the UniProt Swissprot ID, UniProt Swissprot isoform ID, and
#' UniProt TREMBL ID for both the inputted data and the primary transcripts.
#' @importFrom dplyr %>%
#' @importFrom dplyr filter


merge_trans <- function(princ, final_trans, if_aa) {
    prim_alt_lst <- princ %>% dplyr::filter(princ$external_gene_name %in% 
    final_trans$external_gene_name)
    final_pairs <- merge(x = final_trans, y = prim_alt_lst, 
    by.x = "external_gene_name", by.y = "external_gene_name")
    if (if_aa == FALSE) {
        final_pairs <- dplyr::filter(final_pairs, 
            final_pairs$uniprotswissprot.x != "" |
            final_pairs$uniprot_isoform.x != "" |
            final_pairs$uniprotsptrembl.x != "")
        final_pairs <- dplyr::filter(final_pairs, 
            final_pairs$uniprotswissprot.y != "" |
            final_pairs$uniprot_isoform.y != "" |
            final_pairs$uniprotsptrembl.y != "")
        if (nrow(final_pairs) == 0) {
            stop("Please make sure your organism is correct and your transcript 
            IDs are valid and contain no decimal values before continuing.If your 
            IDs are correct and if you recieve this error again then the error is most 
            likely due to Biomart servers being down. Please try again later.")
        }
    }
    if (if_aa == TRUE) {
        final_pairs <- dplyr::filter(final_pairs, final_pairs$uniprotswissprot != "" |
            final_pairs$uniprot_isoform != "" | final_pairs$uniprotsptrembl != "")
        if (nrow(final_pairs) == 0) {
            stop("Please make sure your organism is correct and your transcript 
            IDs are valid and contain no decimal values before continuing.If your 
            IDs are correct and if you recieve this error again then the error is most 
            likely due to Biomart servers being down. Please try again later.")
        }
    }
    return(final_pairs)
}