genambig-class {polysat}

Class "genambig"

Description

Objects of this class store microsatellite datasets in which allele copy number is ambiguous. Genotypes are stored as a two-dimensional list of vectors, each vector containing all unique alleles for a given sample at a given locus. genambig is a subclass of gendata.

Objects from the Class

Objects can be created by calls of the form new("genambig", samples, loci, ...). This automatically sets up a two-dimensional list in the Genotypes slot, with dimnames=list(samples, loci). This array-list is initially populated with the missing data symbol. All other slots are given initial values according to the initialize method for gendata. Data can then be inserted into the slots using the replacement functions (see Accessors).

Slots

Genotypes:

Object of class "array". The first dimension of the array represents and is named by samples, while the second dimension represents and is named by loci. Each element of the array can contain a vector. Each vector should contain each unique allele for the genotype once. If an array element contains a vector of length 1 containing only the symbol that is in the Missing slot, this indicates missing data for that sample and locus.

Description:

Object of class "character". This stores a description of the dataset for the user's convenience.

Missing:

Object of class "ANY". A symbol to be used to indicate missing data in the Genotypes slot. This is the integer -9 by default.

Usatnts:

Object of class "integer". A vector, named by loci. Each element indicates the repeat type of the locus. 2 indicates dinucleotide repeats, 3 indicates trinucleotide repeats, and so on. If the alleles stored in 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 stores the ploidy of each sample. NA indicates unknown ploidy. See Ploidies<- and estimatePloidy for ways to fill this slot.

PopInfo:

Object of class "integer". A vector, named by samples, containing the population identity of each sample.

PopNames:

Object of class "character". A vector containing names for all populations. The position of a population name in the vector indicates the integer used to represent that population in PopInfo.

Extends

Class "gendata", directly.

Methods

For more information on any of these methods, see the help files of their respective generic functions.

deleteLoci

signature(object = "genambig"): Removes columns in the array in the Genotypes slot corresponding to the locus names supplied, then passes the arguments to the method for gendata.

deleteSamples

signature(object = "genambig"): Removes rows in the array in the Genotypes slot corresponding to the sample names supplied, then passes the arguments to the method for gendata.

editGenotypes

signature(object = "genambig"): Each vector in the Genotypes slot is placed into the row of a data frame, along with the sample and locus name for this vector. The data frame is then opened in the Data Editor so that the user can make changes. When the Data Editor window is closed, vectors are extracted back out of the data frame and written to the Genotypes slot.

estimatePloidy

signature(object = "genambig"): Calculates the length of each genotype vector (excluding those with the missing data symbol), and creates a data frame showing the maximum and mean number of alleles per locus for each sample. This data frame is then opened in the Data Editor, where the user may edit ploidy levels. Once the Data Editor is closed, the genambig object is returned with the new values written to the Ploidies slot.

Genotype

signature(object = "genambig"): Retrieves a single genotype vector, as specified by sample and locus arguments.

Genotype<-

signature(object = "genambig"): Replaces a single genotype vector.

Genotypes

signature(object = "genambig"): Retrieves a two-dimensional list of genotype vectors.

Genotypes<-

signature(object = "genambig"): Replaces a one- or two-dimensional list of genotype vectors.

initialize

signature(.Object = "genambig"): When new is called to create a new genambig object, the initialize method sets up a two dimensional list in the Genotypes slot indexed by sample and locus, and fills this list with the missing data symbol. The initialize method for gendata is then called.

isMissing

signature(object = "genambig"): Given a set of samples and loci, each position in the array in the Genotypes slot is checked to see if it matches the missing data value. A single Boolean value or an array of Boolean values is returned.

Loci<-

signature(object = "genambig"): For changing the names of loci. The names are changed in the second dimension of the array in the Genotypes slot, and then the Loci<- method for gendata is called.

Missing<-

signature(object = "genambig"): For changing the missing data symbol. All elements of the Genotypes array that match the current missing data symbol are changed to the new missing data symbol. The Missing<- method for gendata is then called.

Samples<-

signature(object = "genambig"): For changing the names of samples. The names are changed in the first dimension of the array in the Genotypes slot, and then the Samples<- method for gendata is called.

summary

signature(object = "genambig"): Prints the dataset description (Description slot) to the console as well as the number of missing genotypes, then calls the summary method for gendata.

show

signature(object = "genambig"): Prints the data to the console, formatted to make it more legible. The genotype for each locus is shown as the size of each allele, separated by a '/'. The SSR motif length ('Usatnts'), ploidies, population names, and population membership ('PopInfo') are displayed if they exist.

viewGenotypes

signature(object = "genambig"): Prints a tab-delimited table of samples, loci, and genotype vectors to the console.

"["

signature(x = "genambig", i = "ANY", j = "ANY"): For subscipting genambig objects. Should be of the form mygenambig[mysamples, myloci]. Returns a genambig object. The Genotypes slot is replaced by one containing only samples i and loci j. Likewise, the PopInfo and Ploidies slots are truncated to contain only samples i, and the Usatnts slot is truncated to contain only loci j. Other slots are left unaltered.

merge

signature(x = "genambig", y = "genambig"): Merges two genotypes objects together. See merge,genambig,genambig-method.

Author(s)

Lindsay V. Clark, Tyler W. Smith

See Also

gendata, Accessors, merge,genambig,genambig-method

Examples

# display class definition
showClass("genambig")

# create a genambig object
mygen <- new("genambig", samples=c("a", "b", "c", "d"),
             loci=c("L1", "L2", "L3"))
# add some genotypes
Genotypes(mygen)[,"L1"] <- list(c(133, 139, 145), c(142, 154),
                                c(130, 142, 148), Missing(mygen))
Genotypes(mygen, loci="L2") <- list(c(105, 109, 113), c(111, 117),
                                    c(103, 115), c(105, 109, 113))
Genotypes(mygen, loci="L3") <- list(c(254, 258), Missing(mygen),
                                    c(246, 250, 262), c(250, 258))

# see a summary of the object
summary(mygen)
# display some of the genotypes
viewGenotypes(mygen[c("a", "b", "c"),])