genbinary-class: Class "genbinary"
In polysat: Tools for Polyploid Microsatellite Analysis

genbinary-class

R Documentation

Class "genbinary"

Description

This is a subclass of gendata that allows genotypes to be stored as a matrix indicating the presence and absence of alleles.

Objects from the Class

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.

Slots

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.

Extends

Class "gendata", directly.

Methods

Absent: signature(object = "genbinary"): Returns the symbol used to indicate that a given allele is absent in a given sample.
Absent<-: 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.
Genotype: signature(object = "genbinary"): Returns a matrix containing the genotype for a given sample and locus (by a call to Genotypes).
Genotypes: signature(object = "genbinary"): Returns the matrix stored in the Genotypes slot, or a subset as specified by the samples and loci arguments.
Genotypes<-: 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.
initialize: 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.
Missing<-: 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.
Present: signature(object = "genbinary"): Returns the symbol used to indicate that a given allele is present in a given sample.
Present<-: 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.
Samples<-: 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.
Loci<-: 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.
isMissing: 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.
summary: signature(object = "genbinary"): Prints description of dataset and number of missing genotypes, then calls the method for gendata to print additional information.
editGenotypes: 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.
viewGenotypes: signature(object = "genbinary"): Prints the genotype matrix to the console, one locus at a time.
deleteSamples: signature(object = "genbinary"): Removes the specified samples from the genotypes matrix, then calls the method for gendata.
deleteLoci: 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].
estimatePloidy: 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.
merge: signature(x = "genbinary", y = "genbinary"): Merges two genotype objects together. See merge,genbinary,genbinary-method.

Author(s)

Lindsay V. Clark

Examples

# 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

polysat documentation built on Aug. 23, 2022, 5:07 p.m.