# base.freq

##### Base frequencies from DNA Sequences

`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.

##### Usage

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

##### Arguments

- 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

`all = TRUE`

, all counts of bases, ambiguous codes, missing data, and alignment gaps are returned.

##### Details

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.

##### Value

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.

##### See Also

##### Examples

```
# NOT RUN {
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
# }
```

*Documentation reproduced from package ape, version 4.1, License: GPL (>= 2)*