PopGenome (version 2.1.6)

mult.linkage.stats-methods: Multilocus linkage statistics

Description

This generic function calculates the linkage disequilibrium between regions.

Usage

## S3 method for class '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

pairs

permutation matrix of pairwise comparisons

Value

• The return value is a modified object of class "GENOME" -------------------------------------------------------------- The following slots will be modified in the "GENOME" object --------------------------------------------------------------
• 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.

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.

Examples

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