mult.linkage.stats: Multilocus linkage statistics

In pievos101/PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Multilocus linkage statistics

Description

This generic function calculates the linkage disequilibrium between regions.

Usage

## S4 method for signature 'GENOME'
mult.linkage.stats(object,lower.bound=0,upper.bound=1,pairs=FALSE)

Arguments

object	an object of class "GENOME"
lower.bound	sites with minor-allele-frequency>=lower.bound are considered
upper.bound	sites with minor-allele-frequency<=upper.bound are considered
pairs	permutation matrix of pairwise comparisons

Details

pairs is a matrix. Each column contains the pairwise comparison region IDs.

1 1
2 3

compares region 1 with 2, and region 1 with 3.

Value

The return value is a modified object of class "GENOME"

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The following slots will be modified in the "GENOME" object
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mult.Linkage

Some linkage statistics for each pair of regions (R2, P-value, Distance)

The Fisher-Exact-Test is used to calculate the P-values.

Examples

# GENOME.class <- readData("...\Alignments")
# GENOME.class
# GENOME.class <- mult.linkage.stats(GENOME.class)
# show the result:
# [e-mail]
 

pievos101/PopGenome documentation built on May 23, 2024, 7:31 p.m.