getAAMatrix - Build an AA distance matrix
Description¶
getAAMatrix
returns a Hamming distance matrix for IUPAC ambiguous
amino acid characters.
Usage¶
getAAMatrix(gap = 0)
Arguments¶
- gap
- value to assign to characters in the set
c("-", ".")
.
Value¶
A matrix
of amino acid character distances with row and column names
indicating the character pair.
Examples¶
getAAMatrix()
A B C D E F G H I J K L M N P Q R S T V W X Y Z * - .
A 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
B 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 1 0 1 1 1 0 0
C 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
D 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
E 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 0 0
F 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
G 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
H 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
I 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
J 1 1 1 1 1 1 1 1 0 0 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
K 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
L 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1 1 1 1 1 0 1 1 1 0 0
M 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 1 1 0 0
N 1 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 0 0
P 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 0 1 1 1 0 0
Q 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 0 1 0 0
R 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 1 1 1 0 0
S 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 0 1 1 1 0 0
T 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 1 1 0 0
V 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 1 1 1 0 0
W 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0
X 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Y 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 1 0 0
Z 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 0 1 0 0
* 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 0 0
- 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
See also¶
Creates an amino acid distance matrix for seqDist. See getDNAMatrix for nucleotide distances.