base.freq {ape} | R Documentation |
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.
base.freq(x, freq = FALSE, all = FALSE) GC.content(x) Ftab(x, y = NULL)
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 |
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.
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.
Emmanuel Paradis
seg.sites
, nuc.div
(in pegas), DNAbin
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