apex (version 1.0.2)

accessors: multidna Accessors

Description

Accessors for slots in multidna and multiphyDat objects.

Usage

getNumInd(x, ...)
"getNumInd"(x, ...)
"getNumInd"(x, ...)
getNumLoci(x, ...)
"getNumLoci"(x, ...)
"getNumLoci"(x, ...)
getLocusNames(x, ...)
"getLocusNames"(x, ...)
"getLocusNames"(x, ...)
setLocusNames(x) <- value
"setLocusNames"(x) <- value
"setLocusNames"(x) <- value
getNumSequences(x, ...)
"getNumSequences"(x, exclude.gap.only = TRUE, loci = NULL, ...)
"getNumSequences"(x, exclude.gap.only = TRUE, loci = NULL, ...)
getSequenceNames(x, ...)
"getSequenceNames"(x, exclude.gap.only = TRUE, loci = NULL, ...)
"getSequenceNames"(x, exclude.gap.only = TRUE, loci = NULL, ...)
getSequences(x, ...)
"getSequences"(x, loci = NULL, ids = NULL, simplify = TRUE, exclude.gap.only = TRUE, ...)
"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