baseFreq | R Documentation |
baseFreq
computes the frequencies (absolute or relative) of the states
from a sample of sequences.
glance
computes some useful information about the alignment.
baseFreq(obj, freq = FALSE, all = FALSE, drop.unused.levels = FALSE) ## S3 method for class 'phyDat' glance(x, ...)
obj, x |
as object of class phyDat |
freq |
logical, if 'TRUE', frequencies or counts are returned otherwise proportions |
all |
all a logical; if all = TRUE, all counts of bases, ambiguous codes, missing data, and alignment gaps are returned as defined in the contrast. |
drop.unused.levels |
logical, drop unused levels |
... |
further arguments passed to or from other methods. |
baseFreq
returns a named vector and glance
a one row
data.frame
.
Klaus Schliep
phyDat, base.freq, glance
data(Laurasiatherian) data(chloroplast) # base frequencies baseFreq(Laurasiatherian) baseFreq(Laurasiatherian, all=TRUE) baseFreq(Laurasiatherian, freq=TRUE) baseFreq(chloroplast) glance(Laurasiatherian) glance(chloroplast)
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