gtypes.accessors: 'gtypes' Accessors

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

gtypes Accessors

Description

Accessors for slots in gtypes objects.

Usage

## S4 method for signature 'gtypes'
getNumInd(x, by.strata = FALSE, ...)

## S4 method for signature 'gtypes'
getNumLoci(x, ...)

getNumStrata(x, ...)

## S4 method for signature 'gtypes'
getNumStrata(x, ...)

getIndNames(x, ...)

## S4 method for signature 'gtypes'
getIndNames(x, by.strata = FALSE, ...)

getLociNames(x, ...)

## S4 method for signature 'gtypes'
getLociNames(x, ...)

getAlleleNames(x, ...)

## S4 method for signature 'gtypes'
getAlleleNames(x, ...)

getStrataNames(x, ...)

## S4 method for signature 'gtypes'
getStrataNames(x, ...)

getPloidy(x, ...)

## S4 method for signature 'gtypes'
getPloidy(x, ...)

getStrata(x, ...)

## S4 method for signature 'gtypes'
getStrata(x)

setStrata(x) <- value

## S4 replacement method for signature 'gtypes'
setStrata(x) <- value

getSchemes(x, ...)

## S4 method for signature 'gtypes'
getSchemes(x, ...)

setSchemes(x) <- value

## S4 replacement method for signature 'gtypes'
setSchemes(x) <- value

getSequences(x, ...)

## S4 method for signature 'gtypes'
getSequences(
  x,
  as.haplotypes = FALSE,
  seqName = NULL,
  as.multidna = FALSE,
  simplify = TRUE,
  ...
)

getDescription(x, ...)

## S4 method for signature 'gtypes'
getDescription(x, ...)

setDescription(x) <- value

## S4 replacement method for signature 'gtypes'
setDescription(x) <- value

getOther(x, ...)

## S4 method for signature 'gtypes'
getOther(x, value = NULL, ...)

setOther(x, name) <- value

## S4 replacement method for signature 'gtypes'
setOther(x, name) <- value

## S4 method for signature 'gtypes,ANY,ANY,ANY'
x[i, j, k, ..., quiet = TRUE, drop = FALSE]

Arguments

x	a gtypes object.
by.strata	logical - return results by strata?
...	other arguments passed from generics (ignored).
value	value being assigned by accessor.
as.haplotypes	return sequences as haplotypes? If TRUE, contents of @sequences slot are returned. If FALSE, one sequence per individual is returned.
seqName	the name (or number) of a set of sequences from the @sequences slot to return.
as.multidna	return sequences as a multidna object? If FALSE, sequences are returned as a list.
simplify	if 'getSequences()' would return a single locus, return it as a 'DNAbin' object ('TRUE'), or a single element named list ('FALSE').
name	name of the value going into the other list.
i, j, k	subsetting slots for individuals (i), loci (j), or strata (k). See Details for more information.
quiet	suppress warnings about unmatched requested individuals, loci, or strata?
drop	if TRUE the return object will have unused sequences removed.

Details

Indexing a gtypes object with integers, characters, or logicals with the [ operator follows the same rules as normal indexing in R. The order that individuals, loci, and strata are chosen is the order returned by getIndNames, getLocNames, and getStrataNames respectively. If unstratified samples are present, they can be selected as a group either by including NA in the character or numeric vector of the k slot, or by providing a logical vector based on is.na(strata(g)) to the i slot.

Value

nInd

number of individuals

nLoc

number of loci

nStrata

number of strata

indNames

vector of individual/sample names

locNames

vector of locus names

strataNames

vector of strata names for current scheme

ploidy

number of alleles at each locus

other

contents of @other slot

strata

return or modify the current stratification

schemes

return or modify the current stratification schemes

alleleNames

return a list of alleles at each locus

sequences

return the multidna object in the @sequences slot. See getSequences to extract individual genes or sequences from this object

description

return the object's description

Author(s)

Eric Archer [e-mail]

Examples

#--- create a diploid (microsatellite) gtypes object
data(msats.g)
msats.g <- stratify(msats.g, "fine")

getNumStrata(msats.g)
getStrataNames(msats.g)
getNumLoci(msats.g)
getLociNames(msats.g)

# reassign all samples to two randomly chosen strata
new.strata <- sample(c("A", "B"), getNumInd(msats.g), rep = TRUE)
names(new.strata) <- getIndNames(msats.g)
setStrata(msats.g) <- new.strata
msats.g


#--- a sequence example
library(ape)
data(woodmouse)
genes <- list(gene1=woodmouse[,1:500], gene2=woodmouse[,501:965])
x <- new("multidna", genes)
wood.g <- sequence2gtypes(x)
new.strata <- sample(c("A", "B"), getNumInd(wood.g), rep = TRUE)
names(new.strata) <- getIndNames(wood.g)
setStrata(wood.g) <- new.strata
wood.g

# get the multidna sequence object
multi.seqs <- getSequences(wood.g, as.multidna = TRUE)
class(multi.seqs) # "multidna"

# get a list of DNAbin objects
dnabin.list <- getSequences(wood.g)
class(dnabin.list) # "list"

# get a DNAbin object of the first locus
dnabin.1 <- getSequences(wood.g)[[1]]
class(dnabin.1) # "DNAbin"

# getting and setting values in the `other` slot:
getOther(dloop.g)

setOther(dloop.g, "timestamp") <- timestamp()
setOther(dloop.g, "Author") <- "Hoban Washburne"

getOther(dloop.g)
getOther(dloop.g, "timestamp")

setOther(dloop.g, "Author") <- NULL
getOther(dloop.g)

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.