recomb.stats-methods: Recombination statistics

Description Usage Arguments Value References Examples

Description

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

Usage

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## 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

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# 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 !
# [email protected]@Hudson.RM
 

PopGenome documentation built on May 20, 2018, 5:03 p.m.