base.freq computes the frequencies (absolute or relative) of
the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
sample of sequences.
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)
Ftab(x, y = NULL)
Arguments
Value
A numeric vector with names c("a", "c", "g", "t"), or a four by
four matrix with similar dimnames.
Details
The base frequencies are computed over all sequences in the
sample. All missing or unknown sites are discarded from the
computations.
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.
data(woodmouse)
base.freq(woodmouse)
base.freq(woodmouse, TRUE)
Ftab(woodmouse)
Ftab(woodmouse[1, ], woodmouse[2, ]) # same than aboveFtab(woodmouse[14:15, ]) # between the last two