R/scoreByTranscripts.R

In PapenfussLab/RTDetect: Retrotransposed transcript detection from structural variants

#' Ranking matching transcripts
#' @details
#' This is an internal function which returns overlapping transcript names 
#' with ranking scores. 
#' The ranking score is the proportion of exon-exon fusions (intronic 
#' deletion events) detected for a given transcript.
#' @param genes TxDb object of genes. hg19 and hg38 are supported in the 
#' current version.
#' @param transcripts.col A vector of transcript names.
#' @keywords internal
#' @return A dataframe with two columns, tx_name and score. 
.scoreByTranscripts <- function(genes, transcripts.col){
    overlapIntron.df <- as.data.frame(table(transcripts.col)/2)
    colnames(overlapIntron.df) <- c("tx_name", "count") #"sfrc01139" error here!
    overlapIntron.df <- merge(overlapIntron.df, 
                              mcols(GenomicFeatures::transcripts(
                                  genes, columns=c("tx_name","exon_rank"), 
                                  filter=list(tx_name=overlapIntron.df[,1]))))
    return(data.frame(tx_name=overlapIntron.df$tx_name, 
                      score=overlapIntron.df$count / 
                          (vapply(overlapIntron.df$exon_rank, 
                                  length, numeric(1))-1)))
}