base.freq | R Documentation |

`base.freq`

computes the frequencies (absolute or relative) of
the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
sample of sequences.

`GC.content`

computes the proportion of G+C (using the previous
function). All missing or unknown sites are ignored.

`Ftab`

computes the contingency table with the absolute
frequencies of the DNA bases from a pair of sequences.

```
base.freq(x, freq = FALSE, all = FALSE)
GC.content(x)
Ftab(x, y = NULL)
```

`x` |
a vector, a matrix, or a list which contains the DNA sequences. |

`y` |
a vector with a single DNA sequence. |

`freq` |
a logical specifying whether to return the proportions (the default) or the absolute frequencies (counts). |

`all` |
a logical; by default only the counts of A, C, G, and T are
returned. If |

The base frequencies are computed over all sequences in the sample.

For `Ftab`

, if the argument `y`

is given then both `x`

and `y`

are coerced as vectors and must be of equal length. If
`y`

is not given, `x`

must be a matrix or a list and only
the two first sequences are used.

A numeric vector with names `c("a", "c", "g", "t")`

(and possibly
`"r", "m", ...`

, a single numeric value, or a four by four matrix
with similar dimnames.

Emmanuel Paradis

`seg.sites`

, `nuc.div`

(in pegas), `DNAbin`

```
data(woodmouse)
base.freq(woodmouse)
base.freq(woodmouse, TRUE)
base.freq(woodmouse, TRUE, TRUE)
GC.content(woodmouse)
Ftab(woodmouse)
Ftab(woodmouse[1, ], woodmouse[2, ]) # same than above
Ftab(woodmouse[14:15, ]) # between the last two
```

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