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
```

BioPhysConnectoR documentation built on May 30, 2017, 6:46 a.m.

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