locus: General constructor for locus object

In dyerlab/gstudio: Tools Related to the Spatial Analysis of Genetic Marker Data

General constructor for locus object

Description

This function creates an object of type locus, a fundamental type in the gstudio package. Therea re several kinds of loci that can be created.

Usage

locus(x, type = "codom", phased = FALSE)

Arguments

x	The data to be turned into a locus object
type	An indication of what kind of data it is. By default this parameter is missing and this will cause the function to assume that every element of x is an allele in the genotype. blank Default value, uses all passed items as alleles aflp Encoded as 0,1 for absence/presence of bands. column Two columns of alleles separated Pre-separated alleles (with ':'). snp Encoded by the number of minor alleles at the locus. zyme Alleles like zymes (e.g., 12 for '1' and '2' alleles). snp_prob A probabilistic snp call denoted as three posterior likelihoods for AA, AB, and BB as is often found in RAD-seq data.
phased	A flag indicating the the alleles should are of known gametic phase (default=FALSE).

Value

Either a single or vector of objects of type locus.

Author(s)

Rodney J. Dyer [e-mail]

Examples

AA <- locus( c("A","A") )
AB <- locus( c("A","B") )
BB <- locus( c("B","B") )
AC <- locus( c("A","C") )
AD <- locus( c("A","D") )
BC <- locus( c("B","C") )
BD <- locus( c("B","D") )
CC <- locus( c("C","C") )
CD <- locus( c("C","D") )
DD <- locus( c("D","D") )
loci <- c(AA,AB,AC,AD,BB,BC,BD,CC,CD,DD) 
loci

dyerlab/gstudio documentation built on Jan. 17, 2025, 11:17 a.m.