seqalignment: Create seqalignment class object
In bomeara/sleq: sleq

Description Usage Arguments Details Value Examples

Create seqalignment class object

1	seqalignment(x)

`x`	A character matrix

This class is, internally, a list containing character matrix $sequences, $type (a guess at what kind of sequence it is: dna, rna, or aa), and $genes (a character vector with labels for the genes; initialized at "1" for all. However, one cool thing about this class is that if you use [] to access elements, this returns elements from within the $sequences object, not the class object itself.

A seqalignment object

library(ape)
data(woodmouse)
mice.raw <- as.character(woodmouse)
print(mice.raw[1:3, 1:20])
mice.seqalignment <- seqalignment(mice.raw)
print(mice.seqalignment[1:3, 1:20])
print(mice.seqalignment$type)