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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)
a vector, a matrix, or a list which contains the DNA sequences.
a vector with a single DNA sequence.
a logical specifying whether to return the proportions (the default) or the absolute frequencies (counts).
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.
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.
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.
# NOT RUN {
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
# }
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