Description Usage Arguments Details Value See Also Examples
Computes the encoding distance between two encodings.
1 | calc_pi(a, b)
|
a |
encoding (see |
b |
encoding to which |
The encoding distance between a
and b
is defined as the
minimum number of amino acids that have to be moved between subgroups of encoding
to make a
identical to b
(order of subgroups in the encoding and amino
acids in a group is unimportant).
If the parameter prop
is supplied, the encoding distance is normalized by the
factor equal to the sum of distances for each group in a
and the closest group
in b
. The position of a group is defined as the mean value of properties of
amino acids or nucleotides belonging the group.
See the package vignette for more details.
an encoding distance.
calc_si
: compute the similarity index of two encodings.
encoding2df
: converts an encoding to a data frame.
validate_encoding
: validate a structure of an encoding.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # calculate encoding distance between two encodings of amino acids
aa1 = list(`1` = c("g", "a", "p", "v", "m", "l", "i"),
`2` = c("k", "h"),
`3` = c("d", "e"),
`4` = c("f", "r", "w", "y", "s", "t", "c", "n", "q"))
aa2 = list(`1` = c("g", "a", "p", "v", "m", "l", "q"),
`2` = c("k", "h", "d", "e", "i"),
`3` = c("f", "r", "w", "y", "s", "t", "c", "n"))
calc_pi(aa1, aa2)
# the encoding distance between two identical encodings is 0
calc_pi(aa1, aa1)
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