diversity.stats-methods: Diversities
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Usage Arguments Details Value References Examples

A generic function to calculate nucleotide & haplotype diversities.

1 2	## S4 method for signature 'GENOME' diversity.stats(object,new.populations=FALSE,subsites=FALSE,pi=FALSE, keep.site.info=TRUE)

`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.
`pi`	Nei's calculation of pi
`keep.site.info`	stores site specific values in `GENOME.class@region.stats`

The nucleotide diversities have to be devided by GENOME.class@n.sites to give diversities per site.

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.within`	[1,3]	Nucleotide diversity (within the population)
2.	`Pi`	[2]	Diversity from Nei (within the population)
3.	`hap.diversity.within`	[1]	Haplotype diversity (within the population)

[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] Nei, M. (1987). Molecular Evolutionary Genetics. Columbia Univ. Press, New York.

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

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- diversity.stats(GENOME.class)
# GENOME.class <- diversity.stats(GENOME.class,list(1:4,5:10))
# GENOME.class <- diversity.stats(GENOME.class,
# list(c("seq1","seq5","seq3"),c("seq2","seq8")))
# show the result:
# GENOME.class@nuc.diversity.within