mult.linkage.stats: Multilocus linkage statistics

Description Usage Arguments Details Value Examples

Description

This generic function calculates the linkage disequilibrium between regions.

Usage

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## 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.

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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

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

pievos101/PopGenome documentation built on May 16, 2019, 2:54 a.m.