Accessors: Accessor and Replacement Functions for "gendata" Objects

Description

The accessor functions return information that is contained, either directly or indirectly, in the slots of a gendata object. The replacement functions alter information in one or more slots as appropriate.

Usage

Samples(object, populations, ploidies)
Samples(object) <- value
Loci(object, usatnts, ploidies)
Loci(object) <- value
PopInfo(object)
PopInfo(object) <- value
PopNames(object)
PopNames(object) <- value
PopNum(object, popname)
PopNum(object, popname) <- value
Ploidies(object, samples, loci)
Ploidies(object) <- value
Usatnts(object)
Usatnts(object) <- value
Description(object)
Description(object) <- value
Missing(object)
Missing(object) <- value
Present(object)
Present(object) <- value
Absent(object)
Absent(object) <- value
Genotype(object, sample, locus)
Genotype(object, sample, locus) <- value
Genotypes(object, samples = Samples(object), loci = Loci(object))
Genotypes(object, samples = Samples(object), loci = Loci(object)) <- value

Value

PopInfo, PopNames, Missing, Description,

Usatnts, Ploidies and Genotypes simply return the contents of the slots of the same names (or in the case of

Ploidies, object@Ploidies@pld is returned). Samples and

Loci return character vectors taken from the names of other slots (PopInfo and Usatnts, respectively; the initialization and replacement methods ensure that these slots are always named according to samples and loci). PopNum returns an integer vector indicating the population number(s) of the population(s) named in popname.

Genotype returns a single genotype for a given sample and locus, which is a vector whose exact form will depend on the class of

object.

Arguments

object

An object of the class gendata or one of its subclasses.

populations

A character or numeric vector indicating from which populations to return samples. (optional)

ploidies

A numeric vector indicating ploidies, if only samples or loci with a certain ploidy should be returned. (optional)

sample

A character string or number indicating the name or number of the sample whose genotype should be returned.

locus

A character string or number indicating the name or number of the locus whose genotype should be returned.

samples

A character or numeric vector indicating samples for which to return genotypes or ploidies. (optional)

loci

A character or numeric vector indicating loci for which to return genotypes or ploidies. (optional)

usatnts

A numeric vector indicating microsatellite repeat lengths, where only loci of those repeat lengths should be returned. (optional)

popname

Chacter string or vector. The name(s) of the population(s) for which to retrieve or replace the corresponding PopInfo number(s). The replacement function should only be used for one population at a time.

value

For Samples: a character vector of sample names.
For Loci: a character vector of locus names.
For PopInfo: A numeric vector (integer or can be coerced to integer) indicating the population identities of samples.
For PopNames: A character vector indicating the names of populations.
For PopNum: A number (integer or can be coerced to integer) that should be the new population number associated with popname.
For Ploidies: A numeric vector or matrix (integer or can be coerced to integer) indicating the ploidy of each sample, locus, and/or the dataset. See reformatPloidies and "ploidysuper".
For Usatnts: A numeric vector (integer or can be coerced to integer) indicating the repeat type of each microsatellite locus. Dinucleotide repeats should be represented with 2, trinucleotide repeat with 3, and so on. If the alleles for a given locus are already stored in terms of repeat number rather than fragment length in nucleotides, the Usatnts value for that locus should be 1.
For Description: A character string or character vector describing the dataset.
For Missing: A symbol (usually an integer) to be used to indicate missing data.
For Present: A symbol (usually an integer) to be used to indicate the presence of an allele.
For Absent: A symbol (usually an integer) to be used to indicate the absence of an allele.
For Genotype: a vector of alleles, if the object is of class genambig.
For Genotypes: A list of vectors (genotypes), of the same dimensionality as c(length(samples), length(loci)), if the object is of class genambig. If the object is of class genbinary, value should be a matrix, with column names of the form "locus.allele". See Genotypes<-,genbinary-method for more information.

Author

Lindsay V. Clark

Details

Samples<- and Loci<- can only be used to change sample and locus names, not to add or remove samples and loci from the dataset.

For slots that require integer values, numerical values used in replacement functions will be coerced to integers. The replacement functions also ensure that all slots remain properly indexed.

The Missing<- function finds any genotypes with the old missing data symbol and changes them to the new missing data symbol, then assigns the new symbol to the slot that indicates what the missing data symbol is. Present<- and Absent<- work similarly for the genbinary class.

The Genotype access and replacement functions deal with individual genotypes, which are vectors in the genambig class. The Genotypes access and replacement functions deal with lists of genotypes.

The PopInfo<- replacement function also adds elements to PopNames(object) if necessary in order to have names for all of the populations. These will be of the form "Pop" followed by the population number, and can be later edited using PopNames<-.

The PopNum<- replacement function first finds all samples in the population popname, and replaces the number in PopInfo(object) for those samples with value. It then inserts NA into the original PopNames slot that contained popname, and inserts popname into PopNames(object)[value]. If this results in two populations being merged into one, a message is printed to the console.

Examples

Run this code

# create a new genambig (subclass of gendata) object to manipulate
mygen <- new("genambig", samples=c("a", "b", "c"), loci=c("locG",
"locH"))

# retrieve the sample and locus names
Samples(mygen)
Loci(mygen)

# change some of the sample and locus names
Loci(mygen) <- c("lG", "lH")
Samples(mygen)[2] <- "b1"

# describe the dataset
Description(mygen) <- "Example dataset for documentation."

# name some populations and assign samples to them
PopNames(mygen) <- c("PopL", "PopK")
PopInfo(mygen) <- c(1,1,2)
# now we can retrieve samples by population
Samples(mygen, populations="PopL")
# we can also adjust the numbers if we want to make them
# match another dataset
PopNum(mygen, "PopK") <- 3
PopNames(mygen)
PopInfo(mygen)
# change the population identity of just one sample
PopInfo(mygen)["b1"] <- 3

# indicate that both loci are dinucleotide repeats
Usatnts(mygen) <- c(2,2)

# indicate that all samples are tetraploid
Ploidies(mygen) <- 4
# or
Ploidies(mygen) <- rep(4, times = length(Samples(mygen)) * length(Loci(mygen)))
# actually, one sample is triploid
Ploidies(mygen)["c",] <- 3
# view ploidies
Ploidies(mygen)

# view the genotype array as it currently is: filled with missing
# values
Genotypes(mygen)
# fill in the genotypes
Genotypes(mygen, loci="lG") <- list(c(120, 124, 130, 136), c(122, 120),
                                    c(128, 130, 134))
Genotypes(mygen, loci="lH") <- list(c(200, 202, 210), c(206, 208, 210,
                                                        214),
                                    c(208))
# genotypes can also be edited or retrieved by sample
Genotypes(mygen, samples="a")
# fix a single genotype
Genotype(mygen, "a", "lH") <- c(200, 204, 210)
# retrieve a single genotype
Genotype(mygen, "c", "lG")

# change a genotype to being missing
Genotype(mygen, "c", "lH") <- Missing(mygen)
# show the current missing data symbol
Missing(mygen)
# an example of genotypes where one contains the missing data symbol
Genotypes(mygen, samples="c")
# change the missing data symbol
Missing(mygen) <- as.integer(-1)
# now look at the genotypes
Genotypes(mygen, samples="c")

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