Description Usage Arguments Details Value Author(s) References See Also Examples
Computes the sequence entropy of an alignment. It is possible to specify which characters to omit in the computation. The joint entropy is computed using get.entropy2p()
.
1 2 3 4 5 | get.entropy(aln, bool = FALSE, gapchar = "NOGAPCHAR",
verbose = FALSE)
get.entropy2p(aln, bool = FALSE, gapchar = "NOGAPCHAR",
verbose = FALSE)
|
aln |
alignment matrix |
bool |
logical, if TRUE gaps are ignored when computing the entropy of each column of the alignment |
gapchar |
character vector containing the unique set of characters representing gaps in the amino acid sequence |
verbose |
logical, TRUE for getting output messages |
The Shannon (1948) entropy for an alignment is computed as follows:
H(X)=-sum_x p(x)log_2(p(x))
The joint entropy is computed for every possible column pair:
H(X)=-sum_(x,y) p(x,y)log_2(p(x,y))
where X and Y are two columns of the alignment.
Return value for get.entropy()
is a vector containing the entropy for each column.
Return value for get.entropy2p()
is a matrix containing the joint entropies in the lower triangle.
Franziska Hoffgaard
Shannon (1948) The Bell System Technical Journal 27, 379–423.
1 2 3 4 5 6 | aln<-matrix(c("M", "H", "X", "P", "V", "-", "H", "X", "L", "V", "M", "L",
"X", "P", "V"), 3, byrow = TRUE)
h1<-get.entropy(aln, bool = TRUE , gapchar = "-")
h2<-get.entropy(aln)
h3<-get.entropy2p(aln)
|
Loading required package: snow
Loading required package: matrixcalc
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