gtypes.accessors: `gtypes` Accessors

Description

Accessors for slots in '>gtypes objects.

Usage

# S4 method for gtypes
getNumInd(x, by.strata = FALSE, ...)
# S4 method for gtypes
getNumLoci(x, ...)
getNumStrata(x, ...)
# S4 method for gtypes
getNumStrata(x, ...)
getIndNames(x, ...)
# S4 method for gtypes
getIndNames(x, by.strata = FALSE, ...)
getLociNames(x, ...)
# S4 method for gtypes
getLociNames(x, ...)
getAlleleNames(x, ...)
# S4 method for gtypes
getAlleleNames(x, ...)
getStrataNames(x, ...)
# S4 method for gtypes
getStrataNames(x, ...)
getPloidy(x, ...)
# S4 method for gtypes
getPloidy(x, ...)
getStrata(x, ...)
# S4 method for gtypes
getStrata(x)
setStrata(x) <- value
# S4 method for gtypes
setStrata(x) <- value
getSchemes(x, ...)
# S4 method for gtypes
getSchemes(x, ...)
setSchemes(x) <- value
# S4 method for gtypes
setSchemes(x) <- value
getSequences(x, ...)
# S4 method for gtypes
getSequences(x, as.haplotypes = TRUE, seqName = NULL, as.multidna = FALSE, ...)
getDescription(x, ...)
# S4 method for gtypes
getDescription(x, ...)
setDescription(x) <- value
# S4 method for gtypes
setDescription(x) <- value
getOther(x, ...)
# S4 method for gtypes
getOther(x, value = NULL, ...)
setOther(x, name) <- value
# S4 method for gtypes
setOther(x, name) <- value
# S4 method for gtypes,ANY,ANY,ANY
[(x, i, j, k, ..., quiet = TRUE, drop = FALSE)

Arguments

a '>gtypes object.

by.strata

logical - return results by strata?

...

other arguments passed from generics (ignored).

value

value being assigned by accessor.

as.haplotypes

return sequences as haplotypes? If TRUE, contents of @sequences slot are returned. If FALSE, one sequence per individual is returned.

seqName

the name (or number) of a set of sequences from the @sequences slot to return.

as.multidna

return sequences as a '>multidna object? If FALSE, sequences are returned as a list.

name

name of the value going into the other list.

i, j, k

subsetting slots for individuals (i), loci (j), or strata (k). See Details for more information.

quiet

suppress warnings about unmatched requested individuals, loci, or strata?

drop

if TRUE the return object will have unused sequences removed.

Value

nInd: number of individuals
nLoc: number of loci
nStrata: number of strata
indNames: vector of individual/sample names
locNames: vector of locus names
strataNames: vector of strata names for current scheme
ploidy: number of alleles at each locus
other: contents of @other slot
strata: return or modify the current stratification
schemes: return or modify the current stratification schemes
alleleNames: return a list of alleles at each locus
sequences: return the '>multidna object in the @sequences slot. See getSequences to extract individual genes or sequences from this object
description: return the object's description

Details

Indexing a gtypes object with integers, characters, or logicals with the [ operator follows the same rules as normal indexing in R. The order that individuals, loci, and strata are chosen is the order returned by getIndNames, getLocNames, and getStrataNames respectively. If unstratified samples are present, they can be selected as a group either by including NA in the character or numeric vector of the k slot, or by providing a logical vector based on is.na(strata(g)) to the i slot.

Examples

Run this code

# NOT RUN {
#--- create a diploid (microsatellite) gtypes object
data(msats.g)
msats.g <- stratify(msats.g, "fine")

getNumStrata(msats.g)
getStrataNames(msats.g)
getNumLoci(msats.g)
getLociNames(msats.g)

# reassign all samples to two randomly chosen strata
new.strata <- sample(c("A", "B"), getNumInd(msats.g), rep = TRUE)
names(new.strata) <- getIndNames(msats.g)
setStrata(msats.g) <- new.strata
msats.g


#--- a sequence example
library(ape)
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
wood.g <- sequence2gtypes(x)
new.strata <- sample(c("A", "B"), getNumInd(wood.g), rep = TRUE)
names(new.strata) <- getIndNames(wood.g)
setStrata(wood.g) <- new.strata
wood.g

# get the multidna sequence object
multi.seqs <- getSequences(wood.g, as.multidna = TRUE)
class(multi.seqs) # "multidna"

# get a list of DNAbin objects
dnabin.list <- getSequences(wood.g)
class(dnabin.list) # "list"

# get a DNAbin object of the first locus
dnabin.1 <- getSequences(wood.g)[[1]]
class(dnabin.1) # "DNAbin"

# getting and setting values in the `other` slot:
getOther(dloop.g)

setOther(dloop.g, "timestamp") <- timestamp()
setOther(dloop.g, "Author") <- "Hoban Washburne"

getOther(dloop.g)
getOther(dloop.g, "timestamp")

setOther(dloop.g, "Author") <- NULL
getOther(dloop.g)


# }

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