dots.to.bases {ComPairWise} | R Documentation |
dot.to.bases takes an alignment in which bases that match the first taxon are shown with a dot or other character, and replaces them with the base.
dots.to.bases(alignment, matchchar = ".")
alignment |
An alignment object |
matchchar |
Character designating matched base |
A new alignment object, whose elements are
nb |
Number of aligned sequences |
nam |
Character vector of the names of the sequences |
seq |
Character vector of the sequences |
com |
currently always NA; could be a comment |
Designed as an internal function, and is called by read.nexus, but works as a standalone.
TER
read.nexus
, read.phylip
, aln.to.matrix
## The function is currently defined as function (alignment, matchchar = ".") { dotsout <- function(aln.column) { aln.column[aln.column == matchchar] <- aln.column[1] return(aln.column) } aln.new <- aln.to.matrix(alignment, F) aln.new <- apply(aln.new, 2, dotsout) aln.new <- matrix.to.aln(aln.new) alignment$seq <- aln.new$seq return(alignment) }