Accessors {polysat} | R Documentation |
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
Arguments
object |
An object of the class |
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
|
value |
|
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.
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
.
Author(s)
Lindsay V. Clark
See Also
deleteSamples
, deleteLoci
,
viewGenotypes
, editGenotypes
,
isMissing
, estimatePloidy
,
merge,gendata,gendata-method
, gendata
Examples
# 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")