# base.freq

From ape v3.2
by Emmanuel Paradis

##### 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

```
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 3.2, License: GPL (>= 2)*

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