This is a subclass of gendata that allows genotypes to be stored
as a matrix indicating the presence and absence of alleles.
Objects can be created by calls of the form new("genbinary",
samples, loci, ...). After objects are initialized with sample and
locus names, data can be added to slots using the replacement functions.
Genotypes:Object of class "matrix". Row names
of the matrix are sample names. Each column name is a locus name
and an allele separated by a period (e.g.
"loc1.124"); each column represents on allele. The number of
alleles per locus is not limited and can be expanded even after
entering initial data. Each element of the matrix must be equal to
either Present(object), Absent(object), or
Missing(object). These symbols indicate, respectively, that
a sample has an allele, that a sample does not have an allele, or
that data for the sample at that locus are missing.
Present:Object of class "ANY". The integer
1 by default. This symbol is used in the Genotypes
slot to indicate the presence of an allele in a sample.
Absent:Object of class "ANY". The integer
0 by default. This symbol is used in the Genotypes
slot to indicate the absence of an allele in a sample.
Description:Object of class "character". A
character string or vector describing the dataset, for the
convenience of the user.
Missing:Object of class "ANY". The integer
-9 by default. This symbol is used in the Genotypes
slot to indicate that data are missing for a given sample and locus.
Usatnts:Object of class "integer". A vector,
named by loci. This indicates the repeat length of each locus.
2 indicates dinucleotide repeats, 3
indicates trinucleotide repeats, and so on. If the alleles stored
in the column names of the Genotypes slot for a given locus
are already written
in terms of repeat number, the Usatnts value for that locus
should be 1. In other words, all alleles for a locus can be
divided by the number in Usatnts to give alleles expressed in
terms of relative repeat number.
Ploidies:Object of class "integer". A vector,
named by samples. This indicates the ploidy of each sample.
PopInfo:Object of class "integer". A vector,
named by samples. This indicates the population identity of each
sample.
PopNames:Object of class "character". Names
of each population. The position of the population name in the
vector corresponds to the number used to represent that population
in the PopInfo slot.
Class "gendata", directly.
signature(object = "genbinary"): Returns the
symbol used to indicate that a given allele is absent in a given
sample.
signature(object = "genbinary"): Changes the
symbol used to indicate that a given allele is absent in a given
sample. The matrix in the Genotypes slot is searched for
the old symbol, which is replaced by the new. The new symbol is
then written to the Absent slot.
signature(object = "genbinary"): Returns a
matrix containing the genotype for a given sample and locus (by a
call to Genotypes).
signature(object = "genbinary"): Returns the
matrix stored in the Genotypes slot, or a subset as specified
by the samples and loci arguments.
signature(object = "genbinary"): A method
for adding or replacing genotype data in the object. Note that
allele columns cannot be removed from the matrix in the
Genotypes slot using this method, although an entire column
could be filled with zeros in order to effectively remove an
allele from the dataset. If the order of rows in value
(the matrix containing values to be assigned to the
Genotypes slot) is not identical to Samples(object),
the samples argument should be used to indicate row order.
Row names in value are ignored. The loci argument can
be left at the default, even if only a subset of loci are being
assigned. Column names of value are important, and should be
the locus name and allele name separated by a period, as they are in
the Genotypes slot. After checking that the column name is
valid, the method checks for whether the column name already exists or
not in the Genotypes slot. If it does exist, data from that
column are replaced with data from value. If not, a column is
added to the matrix in the Genotypes slot for the new allele. If
the column is new and data are not being written for samples, the method
automatically fills in Missing or Absent symbols for
additional samples, depending on whether or not data for the locus
appear to be missing for the sample or not.
signature(.Object = "genbinary"): Sets up a
genbinary object when new("genbinary") is called. If
samples or loci arguments are missing, these are
filled in with dummy values ("ind1", "ind2", "loc1",
"loc2"). The matrix is then set up in the Genotypes
slot. Sample names are used for row names, and there are zero
columns. The initialize method for gendata is then
called.
signature(object = "genbinary"): Replaces
all elements in matrix in the Genotypes slot containing the
old Missing symbol with the new Missing symbol. The
method for gendata is then called to replace the value in the
Missing slot.
signature(object = "genbinary"): Returns the
symbol used to indicate that a given allele is present in a given
sample.
signature(object = "genbinary"): Changes the
symbol used for indicating that a given allele is present in a given
sample. The symbol is first replaced in the Genotypes slot,
and then in the Present slot.
signature(object = "genbinary"): Changes sample
names in the dataset. Changes the row names in the Genotypes
slot, then calls the method for gendata to change the names in
the PopInfo and Ploidies slots.
signature(object = "genbinary"): Changes locus
names in the dataset. Replaces the locus portion of the column names
in the Genotypes slot, then calls the method for gendata
to change the names in the Usatnts slot.
signature(object = "genbinary"): Returns Boolean
values, by sample and locus, indicating whether genotypes are missing.
If there are any missing data symbols within the genotype, it is
considered missing.
signature(object = "genbinary"): Prints
description of dataset and number of missing genotypes, then calls the
method for gendata to print additional information.
signature(object = "genbinary"): Opens the
genotype matrix in the Data Editor for editing. Useful for making
minor changes, although allele columns cannot be added using this method.
signature(object = "genbinary"): Prints the
genotype matrix to the console, one locus at a time.
signature(object = "genbinary"): Removes the
specified samples from the genotypes matrix, then calls the method for
gendata.
signature(object = "genbinary"): Removes the
specified loci from the genotypes matrix, then calls the method for
gendata.
signature(x = "genbinary", i = "ANY", j = "ANY"):
Subscripting method. Returns a genbinary object with a subset
of the samples and/or loci from x. Usage:
genobject[samples,loci].
signature(object = "genbinary"): Creates a
data frame of mean and maximum number of alleles per sample, which is
then opened in the Data Editor so that the user can manually specify
the ploidy of each sample. Ploidies are then written to the
Ploidies slot of the object.
signature(x = "genbinary", y = "genbinary"): Merges
two genotype objects together. See
merge,genbinary,genbinary-method.
Lindsay V. Clark
gendata, Accessors,
genambig
# show the class definition
showClass("genbinary")
# create a genbinary object
mygen <- new("genbinary", samples = c("indA", "indB", "indC", "indD"),
loci = c("loc1", "loc2"))
Description(mygen) <- "Example genbinary object for the documentation."
Usatnts(mygen) <- c(2,3)
PopNames(mygen) <- c("Maine", "Indiana")
PopInfo(mygen) <- c(1,1,2,2)
Genotypes(mygen) <- matrix(c(1,1,0,0, 1,0,0,1, 0,0,1,1,
1,-9,1,0, 0,-9,0,1, 1,-9,0,1, 0,-9,1,1),
nrow=4, ncol=7, dimnames = list(NULL,
c("loc1.140", "loc1.144", "loc1.150",
"loc2.97", "loc2.100", "loc2.106", "loc2.109")))
# view all of the data in the object
mygen
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