mirna target function

R/target_targetscan.R

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+#' @title Integrate miRNA (MicroRNA) data.
+#'
+#' @description Add miRNA data to MAF file.
+#'
+#' @details This function considers the positions of the variants and looks for 
+#' mirnas targets that are in the same positions to add their names and sites to
+#' them.  
+#'
+#' @param maf Required. MAF data frame (required columns: Chromosome, Start_Position, End_Position).
+#' @param mirna_target Data frame contain miRNA data (required columns: Chromosome, Start_Position, End_Position, miRNA, sites)
+#' @param projection The genome build projection for the variants you are working with (default is grch37)
+#'
+#' @return data frame in MAF format with mirna and sites columns.
+#'
+#' @import dplyr tidyr purrr
+#'
+#' @examples
+#' sample_df = target_targetscan (maf)
+#'
+
+
+target_targetscan <- function(
+                              maf,
+                              mirna_target,
+                              projection = "grch37"
+){
+    if (projection == "grch37") {
+      maf$Chromosome <- gsub("chr", "", maf$Chromosome)
+    } else {
+      # If there is a mix of prefixed and non-prefixed options
+      maf$Chromosome <- gsub("chr", "", maf$Chromosome) 
+      maf$Chromosome <- paste0("chr", maf$Chromosome)
+    }
+    if (missing(mirna_target)){
+      mirna_target <- GAMBLR.data::mirna_targetscan
+    }
+    mirna <- mirna_target %>%
+            arrange(
+              Chromosome,
+              Start_Position,
+              End_Position
+            )
+    maf_mi <- pmap(
+                list(
+                  maf$Chromosome,
+                  maf$Start_Position,
+                  maf$End_Position
+                ),
+                function(
+                  chrom,
+                  start_pos,
+                  end_pos
+                ) {
+                    match <- mirna %>%
+                          filter(
+                            (Chromosome == chrom) &
+                              (Start_Position <= start_pos &
+                                 End_Position >= start_pos) |
+                                  (Start_Position > start_pos &
+                                     Start_Position <= end_pos
+                                   )
+                          )
+                    if (nrow(match) == 0) {
+                      data.frame(
+                        Chromosome = chrom,
+                        Start_Position = start_pos,
+                        End_Position = end_pos,
+                        miRNA = NA,
+                        sites = NA
+                      )
+                    } else {
+                      match %>%
+                        mutate(
+                          Chromosome = chrom,
+                          Start_Position = start_pos,
+                          End_Position = end_pos) %>%
+                            select(
+                              Chromosome,
+                              Start_Position,
+                              End_Position,
+                              miRNA,
+                              sites
+                            )
+                    }
+                }
+              )
+    mi_match <- bind_rows(maf_mi)
+    output <- left_join(
+                maf,
+                mi_match,
+                relationship = "many-to-many"
+              ) %>%
+                distinct()
+    return(output)
+}