DNA distance matrices and phylogenetic trees

2022-11-21 17:38:06 -06:00 · 2022-11-21 17:38:06 -06:00 · 57d2a94faa
commit 57d2a94faa
parent 056dcb299b
2 changed files with 62 additions and 0 deletions
--- a/Schrick-Noah_CS-6643_Lab-10.docx
+++ b/Schrick-Noah_CS-6643_Lab-10.docx
--- a/msaUtils.R
+++ b/msaUtils.R
@ -0,0 +1,62 @@
+msaConvert <- function(x, type=c("seqinr::alignment",
+                                 "bios2mds::align",
+                                 "ape::AAbin",
+                                 "ape::DNAbin",
+                                 "phangorn::phyDat"))
+{
+      type <- match.arg(type)
+      
+      if (!is(x, "MultipleAlignment"))
+            stop("x must be a 'MultipleAlignment' object")
+      
+      xn <- as.character(unmasked(x))
+      
+      if (type == "seqinr::alignment")
+      {
+            out <- list(nb=length(xn),
+                        nam=names(xn),
+                        seq=unname(xn),
+                        com=NA)
+            
+            class(out) <- "alignment"
+      }
+      else if (type == "bios2mds::align")
+      {
+            out <- .Call("SplitCharVector2List", xn)
+            names(out) <- names(xn)
+            class(out) <- "align"
+      }
+      else if (type == "ape::AAbin")
+      {
+            if (!is(x, "AAMultipleAlignment"))
+                  stop("conversion to 'ape::AAbin' only supported for ",
+                       "amino acid sequences")
+            
+            out <- .Call("SplitCharVector2Matrix", xn, "X")
+            rownames(out) <- names(xn)
+            class(out) <- "AAbin"
+      }
+      else if (type == "ape::DNAbin")
+      {
+            if (!is(x, "DNAMultipleAlignment"))
+                  stop("conversion to 'ape::DNAbin' only supported for ",
+                       "DNA sequences")
+            
+            out <- .Call("SplitCharVector2Matrix", tolower(xn), "n")
+            rownames(out) <- names(xn)
+            class(out) <- "DNAbin"
+      }
+      else if (type == "phangorn::phyDat")
+      {
+            if (!is(x, "DNAMultipleAlignment"))
+                  stop("conversion to 'phangorn::phyDat' only supported for ",
+                       "DNA sequences")
+            
+            if (requireNamespace("phangorn", quietly=TRUE))
+                  out <- phangorn::as.phyDat(x)
+            else
+                  stop("conversion to 'phyDat' requires package 'phangorn'")
+      }
+      
+      out
+}