This function computes the relative frequencies (i.e. proportions) of
the four DNA bases (adenine, cytosine, guanine, and thymidine) from a
sample of sequences.
Usage
base.freq(x, freq = FALSE)
Arguments
x
a vector, a matrix, or a list which contains the DNA
sequences.
freq
a logical specifying whether to return the proportions
(the default) or the absolute frequencies (counts).
Value
A numeric vector storing the relative frequencies with names
c("a", "c", "g", "t").
Details
The base frequencies are computed over all sequences in the
sample. All missing or unknown sites are discarded from the
computations.