aue.sort: Ordering the content of cells in a matrix. Ordering alleles...

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

Description

This program takes a matrix and orders the content of each cell. It was specially designed for genetic data, but can be used with any data that can be rearranged by the function order. The arguments ploidy and ncode determine the mode of ordering the data. The cells corresponding to each individual i and loci j are ordered in ascending order in default option (it can be passed decreasing = TRUE as argument, if descending order is desired). For example, a locus with ploidy = 2 and ncod =1, coded as 51, for an individual, will be recoded as 15. A locus with ploidy = 3 and coded as 143645453, will be recoded as 143453645 (alleles 143, 454 and 645).

Usage

aue.sort(X, ncod = NULL, ploidy = 2, sep.loc = "", chk.plocod = TRUE, ...)

Arguments

X	Any matrix with content to order.
ncod	Number of digits coding each allele (e.g., 1: x, 2: xx, 3: xxx, etc.). If NULL, ncode will we obtained from the ploidy and the maximum number of characters in the data cells.
ploidy	Ploidy of the data.
sep.loc	Character string separating alleles.
chk.plocod	Defalult TRUE. The function checks coherence in ploidy and number of digits coding alleles.
...	Additional arguments passed to order

Author(s)

Leandro Roser [e-mail]

Examples

## Not run: 

# Example 1----------------------

geno <- c(12, 52, 62, 45, 54, 21)
geno <- matrix(geno, 3, 2)

# ordering the data
aue.sort(geno, ploidy = 2)

# decreasing sort order
aue.sort(geno, ploidy = 2, decreasing = TRUE)


# Example 2----------------------

geno2 <- c(123456, 524556, 629359, 459459, 543950, 219405)
geno2 <- matrix(geno2, 3, 2)

# ordering the data as diploid
aue.sort(geno2, ploidy = 2)  # the data is ordered using blocks of 3 characters

# ordering the data as triploid
aue.sort(geno2, ploidy = 3)  # the data is ordered using blocks of 2 characters

# error: the ploidy and the number of characters are not congruent
aue.sort(geno2, ploidy = 5) 

# error: the ploidy and the number of characters are not congruent
aue.sort(geno2, ploidy = 5)


# Example 3----------------------

# any character data
generic <- c("aldk", "kdbf", "ndnd", "ndkd")
generic <- matrix(generic, 2, 2)
aue.sort(generic, ploidy = 2) 
aue.sort(generic, ploidy = 4)


## End(Not run)

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