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PopGenome (version 2.1.6)

recomb.stats-methods: Recombination statistics

Description

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

Usage

## S3 method for class 'GENOME':
recomb.stats(object,new.populations=FALSE,subsites=FALSE)
## S3 method for class '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. "int

Value

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

Run this code
# 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 !
# GENOME.class@region.stats@Hudson.RM

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