R/tableMutationDetails.R

In chapmandu2/CollateralVulnerability2016: Collateral Vulnerability Pipeline

#' Mutation details table
#'
#' Extracts mutation details from the SQLite database for a given gene
#'
#' @param con A \code{SQLiteConnection} object
#' @param input_gene An ensembl gene ID
#' @return A data frame
#' @export
tableMutationDetails <- function(con, input_gene) {

    dplyr::src_sqlite(con@dbname) %>%
        dplyr::tbl('mutation_analysis_data') %>%
        dplyr::filter(gene_id == input_gene) %>%
        dplyr::select(Hugo_Symbol, sample_id, Variant_Classification, Protein_Change) %>%
        dplyr::collect() %>%
        as.data.frame()

}