mult.linkage.stats: Multilocus linkage statistics
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Usage Arguments Details Value Examples

This generic function calculates the linkage disequilibrium between regions.

1 2	## S4 method for signature 'GENOME' mult.linkage.stats(object,lower.bound=0,upper.bound=1,pairs=FALSE)

`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

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.

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.

# GENOME.class <- readData("...\Alignments")
# GENOME.class
# GENOME.class <- mult.linkage.stats(GENOME.class)
# show the result:
# GENOME.class@mult.Linkage

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.