calc.R2-methods: Linkage statistics (R2, P-value, Distance)
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Usage Arguments Details Value Examples

This generic function calculates some linkage disequilibrium statistics.

1 2	## S4 method for signature 'GENOME' calc.R2(object,subsites=FALSE,lower.bound=0,upper.bound=1)

`object`	an object of class `"GENOME"`
`subsites`	same as in the other modules
`lower.bound`	sites with minor-allele-frequency>=lower.bound are considered
`upper.bound`	sites with minor-allele-frequency<=upper.bound are considered

Note, the pairwise comparisons are computed via combn(n.snps,2).

The slot GENOME.class@region.stats@linkage.disequilibrium will be filled.
(R2,P-value,Distance)
Fisher's Exact Test is used for the P-values.

# GENOME.class <- readData("...\Alignments")
# GENOME.class
# GENOME.class <- calc.R2(GENOME.class)
# show the result:
# GENOME.class@region.stats@linkage.disequilibrium
# [[x]][[y]] x:region, y:population