PopGenome (version 2.7.5)

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

Description

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

Usage

# S4 method for 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

Value

Returned value is a modified object of class "GENOME" --------------------------------------------------------- The following slots will be modified in the "GENOME" object ---------------------------------------------------------

	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

Details

The nucleotide diversities have to be devided by [e-mail] to give diversities per site.

References

[x]

Examples

# NOT RUN {
# GENOME.class <- readData("\home\Alignments")
# set.populations
# GENOME.class <- calc.fixed.shared(GENOME.class)
# }