calc.fixed.shared-methods: Fixed and shared polymorphisms

Description Usage Arguments Details Value References Examples

Description

A generic function to calculate the number of fixed and shared polymorphisms.

Usage

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## S4 method for signature 'GENOME'
calc.fixed.shared(object,
subsites=FALSE,
new.populations=FALSE,
fixed.threshold=1,
fixed.threshold.fst=1)

Arguments

object

An object of class "GENOME"

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.
"intergenic" : SNPs in intergenic regions.

new.populations

list of populations. default=FALSE

fixed.threshold

Polymorphisms are considered as fixed >= threshold value

fixed.threshold.fst

Polymorphisms are considered as fixed >= threshold value

Details

The nucleotide diversities have to be devided by [email protected] to give diversities per site.

Value

Returned 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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Slot Reference Description
1. n.fixed.sites [x] Number of fixed sites
2. n.shared.sites [x] Number of shared sites
3. n.monomorphic.sites [x] Number of monomorphic sites

References

[x]

Examples

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# GENOME.class <- readData("\home\Alignments")
# set.populations
# GENOME.class <- calc.fixed.shared(GENOME.class)

pievos101/PopGenome documentation built on May 16, 2019, 2:54 a.m.