accessors | R Documentation |
Accessors for slots in multidna and multiphyDat objects.
getNumInd(x, ...)
## S4 method for signature 'multidna'
getNumInd(x, ...)
## S4 method for signature 'multiphyDat'
getNumInd(x, ...)
getNumLoci(x, ...)
## S4 method for signature 'multidna'
getNumLoci(x, ...)
## S4 method for signature 'multiphyDat'
getNumLoci(x, ...)
getLocusNames(x, ...)
## S4 method for signature 'multidna'
getLocusNames(x, ...)
## S4 method for signature 'multiphyDat'
getLocusNames(x, ...)
setLocusNames(x) <- value
## S4 replacement method for signature 'multidna'
setLocusNames(x) <- value
## S4 replacement method for signature 'multiphyDat'
setLocusNames(x) <- value
getNumSequences(x, ...)
## S4 method for signature 'multidna'
getNumSequences(x, exclude.gap.only = TRUE,
loci = NULL, ...)
## S4 method for signature 'multiphyDat'
getNumSequences(x, exclude.gap.only = TRUE,
loci = NULL, ...)
getSequenceNames(x, ...)
## S4 method for signature 'multidna'
getSequenceNames(x, exclude.gap.only = TRUE,
loci = NULL, ...)
## S4 method for signature 'multiphyDat'
getSequenceNames(x, exclude.gap.only = TRUE,
loci = NULL, ...)
getSequences(x, ...)
## S4 method for signature 'multidna'
getSequences(x, loci = NULL, ids = NULL,
simplify = TRUE, exclude.gap.only = TRUE, ...)
## S4 method for signature 'multiphyDat'
getSequences(x, loci = NULL, ids = NULL,
simplify = TRUE, exclude.gap.only = TRUE, ...)
x |
a multidna or multiphyDat object. |
... |
further arguments passed on to other functions. |
value |
a replacement value for the slot. |
exclude.gap.only |
logical. Remove or ignore sequences containing all gaps? |
loci |
a character, numeric, or logical vector identifying which loci to return. |
ids |
a character, numeric, or logical vector identifying which sequences to return within a locus. |
simplify |
logical. If |
Returns the number of individuals.
Returns the number of loci.
Returns the names of each locus.
Sets the names of each locus.
Returns the number of sequences in each locus.
Returns the names of individual sequences at each locus.
Returns sequences of specified loci and individuals.
returns the information stored in a slot, see details.
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