diversity.stats.between-methods: Diversities

In pievos101/PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Diversities

Description

A generic function to calculate nucleotide & haplotype diversities between populations (dxy).

Usage

## S4 method for signature 'GENOME'
diversity.stats.between(object,new.populations=FALSE,subsites=FALSE,keep.site.info=FALSE,
haplotype.mode=FALSE, nucleotide.mode=TRUE)

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. "intergenic" : SNPs in intergenic regions.
keep.site.info	Store SNP specific values in the region.stats
haplotype.mode	Haplotype Diversities
nucleotide.mode	Nucleotide Diversities

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.	nuc.diversity.between	[1,3]	Nucleotide diversity (between the population)
2.	hap.diversity.between	[1]	Haplotype diversity (between the population)

References

[1] Hudson, R. R., M. Slatkin, and W.P. Maddison (1992). Estimating of levels of gene flow from DNA sequence data. Gentics 13(2),583-589

[2] Wakeley, J. (1996).The Variance of Pairwise Nucleotide Differences in Two Populations with Migration. THEORETICAL POPULATION BIOLOGY. 49, 39-57.

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- diversity.stats.between(GENOME.class)
# GENOME.class <- set.populations(GENOME.class, list(...))
# GENOME.class <- diversity.stats.between(GENOME.class)
# GENOME.class <- diversity.stats(GENOME.class,
# list(c("seq1","seq5","seq3"),c("seq2","seq8")))
# show the result:
# [e-mail]

pievos101/PopGenome documentation built on Feb. 24, 2023, 7:11 a.m.