accessors {apex}

multidna Accessors

Description

Accessors for slots in multidna and multiphyDat objects.

Usage

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, ...)

Arguments

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 FALSE, always return a list of DNAbin sequences. If TRUE and only one locus has been requested, return a single DNAbin object.

Details

getNumInd

Returns the number of individuals.

getNumLoci

Returns the number of loci.

getLocusNames

Returns the names of each locus.

setLocusNames

Sets the names of each locus.

getNumSequences

Returns the number of sequences in each locus.

getSequenceNames

Returns the names of individual sequences at each locus.

getSequences

Returns sequences of specified loci and individuals.

Value

returns the information stored in a slot, see details.