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
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.
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