MMD_Rn {MMD}

Loci redundancy in sequences

Description

Loci redundancy in sequences

Usage

MMD_Rn(datafile, popfile, NL, sourcenames, verbose = FALSE)

Arguments

datafile

character; Name of the file *.csv (with full path in the file system) containing the genotypes (features) of individuals.

popfile

character; Name of the file *.pop (with full path in the file system) containing the genotypes (features) of individuals.

NL

integer; number of loci. If larger than the number of available loci in the data set, NL is reduced to the maximum available number of loci.

sourcenames

a character vector listing the names of the sources.

verbose

boolean (TRUE/FALSE) for the display of a progress bar (Default FALSE)

Value

A list with

1. Number of loci.

2. Number of individuals in sources.

3. Data frame with proportional weight of each population, qs.

4. Number of alleles in the dataset.

5. Value of the alleles in the dataset.

6. Dataframe with two columns: (1) Index of locus. (2) Rn for loci in the original dataset.

7. numerical; index of loci with increasing Rn.

8. Dataframe with two columns: (1) Index of loci sorted by increasing Rn. (2) Value of Rn in increasing order.

9. Runtime.

Author(s)

Francisco J. Perez-Reche (Univeristy of Aberdeen)

Examples

## This example uses a small dataset stored in the MMD package
datafile <- system.file("extdata", "Campylobacter_10SNP_HlW.csv", package = "MMD")
popfile <- system.file("extdata", "Campylobacter_10SNP_HlW.pop", package = "MMD")

NL <- 100
sourcenames <- c("Cattle","Chicken","Pig","Sheep","WB")

RedundancyLoci <- MMD_Rn(datafile,popfile,NL,sourcenames)

## See more detailed examples in the vignette.