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

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

Description

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

Usage

## 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 [e-mail] 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

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

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