recomb.stats-methods: Recombination statistics

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

Description

This generic function calculates the Four-Gamete test (Hudson 1985).

Usage

## S4 method for signature 'GENOME'
recomb.stats(object,new.populations=FALSE,subsites=FALSE)
## S4 method for signature 'GENOME'
get.recomb(object)

Arguments

object	an object of class "GENOME"
new.populations	list of populations. default:FALSE
subsites	"transitions": SNPs that are transitions. "transversions": SNPs that are transversions. "syn": synonymous sites. "nonsyn": nonsynonymous sites. "exon": SNPs in exon regions. "intron": SNPs in intron regions. "coding": SNPs in coding regions (CDS). "utr": SNPs in UTR regions. "gene": SNPs in genes. default:FALSE

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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Hudson.RM

Four-gamete test

References

Hudson, R. K. (1985). Statistical Properties of the Number of Recombination Events in the History of a Sample of DNA Sequences Genetics 111 (1): 147-164.

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- recomb.stats(GENOME.class)
# GENOME.class <- recomb.stats(GENOME.class,list(1:7,8:12))
# show the result:
# recomb.values <- get.recomb(GENOME.class)
# recomb.values[[1]] # first population !
# [e-mail]@Hudson.RM
 

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