sidier (version 2.2)

pop.dist: Distances among populations

Description

This function computes the among population distance matrix based on the frequency of haplotypes per population and the among haplotypes distance matrix. It is mandatory to define haplotype and population names in the input file. See example for details.

Usage

pop.dist(DistFile = NA, distances = NA, HaploFile = NA, Haplos = NA,
 outType = "O", logfile = TRUE, saveFile = TRUE, NameIniPopulations
 = NA, NameEndPopulations = NA, NameIniHaplotypes = NA,
 NameEndHaplotypes = NA)

Arguments

DistFile

the name of the file containing the distance matrix among haplotypes to be analysed.

distances

the distance matrix among haplotypes (stored in memory) to be analysed.

HaploFile

the name of the file containing the matrix with the number of haplotypes found per population.

Haplos

the name of the matrix (stored in memory) containing the number of haplotypes found per population.

outType

a strig; the format of output matrix. "L" for lower diagonal hemi-matrix; "7" for upper diagonal hemi-matrix; "O" for both hemi-matrices (default).

logfile

a logical; if TRUE (default), it saves a file containing matrix names used (inputDist and HaploFile)

saveFile

a logical; if TRUE (default), function output is saved as a text file.

NameIniPopulations

a numeric indicating the position of the initial character of population names within the individual name in the matrix containing the number of haplotypes found per population (see exaple for details).

NameEndPopulations

a numeric indicating the position of the last character of population names within the individual name in the matrix containing the number of haplotypes found per population (see exaple for details).

NameIniHaplotypes

a numeric indicating the position of the initial character of haplotype names within the individual name in the distance matrix (see exaple for details).

NameEndHaplotypes

a numeric indicating the position of the last character of haplotype names within the individual name in the distance matrix (see exaple for details).

Value

• A matrix containing the genetic distances among populations, based on the haplotype distances and their frequencies per populations.

Details

Each element in the population distance matrix is calculated as the arithmetic mean of the distances among all the sequences sampled in the two compared populations, as follows: $$dist(i,j) = \frac{\sum_{k=1}^{m}{\sum_{l=1}^{n}{dist(H_{ki},H_{lj})}}}{m*n}$$ where dist(i,j) represents the distance between populations i and j, m and n are the number of sequences in populations i and j, respectively, and dist(H_{ki},H_{lj}) is the distance between the k-th sequence found in population i and the l-th sequence found in population j.

Examples

cat("H1 H2 H3 H4 H5",
"Population1 1 2 1 0 0",
"Population2 0 0 0 4 1",
"Population3 0 1 0 0 3",
     file = "4_Example3_HapPerPop_Weighted.txt", sep = "")


cat("H1 H2 H3 H4 H5",
"H1 0 1 2 3 1",
"H2 1 0 3 4 2",
"H3 2 3 0 1 1",
"H4 3 4 1 0 2",
"H5 1 2 1 2 0",
     file = "4_Example3_IndelDistanceMatrixMullerMod.txt", sep = "")
     example3_2 <- read.table("4_Example3_IndelDistanceMatrixMullerMod.txt"
,header=TRUE)

# Checking row names to estimate NameIniHaplotypes,NameEndHaplotypes:
 row.names(read.table(file="4_Example3_IndelDistanceMatrixMullerMod.txt"))
## [1] "H1" "H2" "H3" "H4" "H5" NameIniHaplotypes=1. NameEndHaplotypes=2
# Checking row names to estimate NameIniPopulations, and NameEndPopulations
 row.names(read.table(file="4_Example3_HapPerPop_Weighted.txt"))
## [1] "Population1" "Population2" "Population3"
## NameIniPopulations=1 NameEndPopulations =11


# Reading files. Distance matrix must contain haplotype names. Abundance
# matrix must contain both, haplotype and population names:

pop.dist (DistFile="4_Example3_IndelDistanceMatrixMullerMod.txt", 
HaploFile="4_Example3_HapPerPop_Weighted.txt", outType="O",
NameIniHaplotypes=1,NameEndHaplotypes=2,NameIniPopulations=1,
NameEndPopulations=11)