Conversion among Sequence Formats
These functions transform several DNA formats into the phyDat format.
allSitePattern generates an alignment of all possible site patterns.
phyDat(data, type = "DNA", levels = NULL, return.index = TRUE, ...)
as.phyDat(x, ...)
## S3 method for class 'factor'
as.phyDat(x, ...)
## S3 method for class 'DNAbin'
as.phyDat(x, ...)
## S3 method for class 'alignment'
as.phyDat(x, type = "DNA", ...)
phyDat2alignment(x)
## S3 method for class 'MultipleAlignment'
as.phyDat(x, ...)
## S3 method for class 'phyDat'
as.MultipleAlignment(x, ...)
acgt2ry(obj)
## S3 method for class 'phyDat'
as.character(x, allLevels = TRUE, ...)
## S3 method for class 'phyDat'
as.data.frame(x, ...)
## S3 method for class 'phyDat'
as.DNAbin(x, ...)
## S3 method for class 'phyDat'
as.AAbin(x, ...)
baseFreq(obj, freq = FALSE, all = FALSE, drop.unused.levels = FALSE)
## S3 method for class 'phyDat'
subset(x, subset, select, site.pattern = TRUE, ...)
## S3 method for class 'phyDat'
x[i, j, ..., drop = FALSE]
## S3 method for class 'phyDat'
unique(x, incomparables = FALSE, identical = TRUE, ...)
removeUndeterminedSites(x, ...)
allSitePattern(n, levels = c("a", "c", "g", "t"), names = NULL)
genlight2phyDat(x, ambiguity = NA)
## S3 method for class 'phyDat'
image(x, ...)data |
An object containing sequences. |
type |
Type of sequences ("DNA", "AA", "CODON" or "USER"). |
levels |
Level attributes. |
return.index |
If TRUE returns a index of the site patterns. |
... |
further arguments passed to or from other methods. |
x |
An object containing sequences. |
obj |
as object of class phyDat |
allLevels |
return original data. |
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 |
subset |
a subset of taxa. |
select |
a subset of characters. |
site.pattern |
select site pattern or sites. |
i, j |
indices of the rows and/or columns to select or to drop. They may be numeric, logical, or character (in the same way than for standard R objects). |
drop |
for compatibility with the generic (unused). |
incomparables |
for compatibility with unique. |
identical |
if TRUE (default) sequences have to be identical, if FALSE sequences are considered duplicates if distance between sequences is zero (happens frequently with ambiguous sites). |
n |
Number of sequences. |
names |
Names of sequences. |
ambiguity |
character for ambiguous character and no contrast is provided. |
If type "USER" a vector has to be give to levels. For example
c("a", "c", "g", "t", "-") would create a data object that can be used in
phylogenetic analysis with gaps as fifth state. There is a more detailed
example for specifying "USER" defined data formats in the vignette
"phangorn-specials".
allSitePattern returns all possible site patterns and can be useful
in simulation studies. For further details see the vignette
phangorn-specials.
The generic function c can be used to to combine sequences and
unique to get all unique sequences or unique haplotypes.
acgt2ry converts a phyDat object of nucleotides into an binary
ry-coded dataset.
The functions return an object of class phyDat.
Klaus Schliep klaus.schliep@gmail.com
data(Laurasiatherian) class(Laurasiatherian) Laurasiatherian # base frequencies baseFreq(Laurasiatherian) baseFreq(Laurasiatherian, all=TRUE) baseFreq(Laurasiatherian, freq=TRUE) # subsetting phyDat objects # the first 5 sequences subset(Laurasiatherian, subset=1:5) # the first 5 characters subset(Laurasiatherian, select=1:5, site.pattern = FALSE) # subsetting with [] Laurasiatherian[1:5, 1:20] # short for subset(Laurasiatherian, subset=1:5, select=1:20, site.pattern = FALSE) # the first 5 site patterns (often more than 5 characters) subset(Laurasiatherian, select=1:5, site.pattern = TRUE) # transform into old ape format LauraChar <- as.character(Laurasiatherian) # and back Laura <- phyDat(LauraChar) all.equal(Laurasiatherian, Laura) # Compute all possible site patterns # for nucleotides there $4 ^ (number of tips)$ patterns allSitePattern(5)
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