eco.convert: Conversion utility for genetic data

In EcoGenetics: Management and Exploratory Analysis of Spatial Data in Landscape Genetics

Description

This function interconverts genetic data among matrix format (one locus or one allele per column) and list format (one locus or one allele per column).

Usage

eco.convert(
  X,
  input = c("matrix", "alleles.matrix", "list", "alleles.list"),
  output = c("matrix", "alleles.matrix", "list", "alleles.list"),
  ncod = NULL,
  ploidy = 2,
  sep.in,
  sep.out,
  chk.names = TRUE,
  chk.plocod = TRUE
)

Arguments

X	Input data.
input	Input data format.
output	Output data format.
ncod	Number of digits coding each allele.
ploidy	Ploidy of the data.
sep.in	Character separating alleles in the input data if present.
sep.out	Character separating alleles in the output data. Default option do not separate alleles.
chk.names	Defalult TRUE. The function makes checks of individuals and loci names during conversion.
chk.plocod	Defalult TRUE. The function checks coherence in/between ploidy and number of digits coding alleles for loci data during conversion.

Author(s)

Leandro Roser [e-mail]

Examples

## Not run: 

data(eco3)

# One allele per column
loc2al <- eco.convert(eco3[["G"]], "matrix", "alleles.matrix", ploidy = 2)
loc2al     

# Inverse operation (collapse alleles into locus)
al2loc <- eco.convert(loc2al, "alleles.matrix", "matrix", ploidy = 2)
al2loc

# Separating alleles with a character string
loc2loc <- eco.convert(eco3[["G"]], "matrix", "matrix", ploidy = 2, sep.out = "/")
loc2loc

# Inverse operation (removing separator)
loc2loc.nosep <- eco.convert(loc2loc, "matrix", "matrix", ploidy = 2, sep.in = "/", sep.out = "")
loc2loc.nosep

# Locus to list
loc2list <- eco.convert(eco3[["G"]], "matrix", "list", ploidy = 2)
loc2list

# Locus to allele list
al2list <- eco.convert(eco3[["G"]], "matrix",  "alleles.list", ploidy = 2)
al2list

# The inverse operations are also defined. All the formats are interconvertible.
# Locus operations have defined a within operation (matrix to matrix, list to list), 
# with the purpose of put/remove separators between alleles. The program accepts any ploidy level. 



## End(Not run)

EcoGenetics documentation built on July 8, 2020, 5:46 p.m.