ORFik addition

DESCRIPTION

@@ -32,6 +32,7 @@ Imports:
     ggplot2,
     ggtree,
     magrittr,
+    ORFik,
     phangorn,
     purrr,
     readr,

NAMESPACE

@@ -64,6 +64,7 @@ importFrom(DECIPHER,AlignSeqs)
 importFrom(DECIPHER,DistanceMatrix)
 importFrom(GenomicRanges,GRanges)
 importFrom(IRanges,ranges)
+importFrom(ORFik,findORFs)
 importFrom(ape,as.DNAbin)
 importFrom(cowplot,draw_label)
 importFrom(cowplot,get_legend)

R/find_longest_orf.R

@@ -9,6 +9,7 @@
 #' @importFrom Biostrings DNAStringSet
 #' @importFrom GenomicRanges GRanges
 #' @importFrom IRanges ranges
+#' @importFrom ORFik findORFs
 #' @import dplyr tibble tidyr
 #'
 #' @examples
@@ -18,7 +19,7 @@
 #' @export
 find_longest_orf <- function(seqs = DNAStringSet) {
   # Find ORFs in the sequences, return longest ORF, and convert to a vector
-  orfs <- findORFs(seqs, longestORF = TRUE, startCodon = startDefinition(6)) %>%
+  orfs <- ORFik::findORFs(seqs, longestORF = TRUE, startCodon = startDefinition(6)) %>%
     unlist(use.names = TRUE)
   # Convert the ORFs to a GRanges object
   orfs <- GRanges(seqnames = names(seqs)[as.integer(names(orfs))],