PopGenome (version 2.7.2)

diversity.stats-methods: Diversities

Description

A generic function to calculate nucleotide & haplotype diversities.

Usage

# S4 method for GENOME
diversity.stats(object,new.populations=FALSE,subsites=FALSE,pi=FALSE, keep.site.info=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.

pi

Nei's calculation of pi

keep.site.info

stores site specific values in [e-mail]

Value

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

	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)

Details

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

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] 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.

Examples

# NOT RUN {
# 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:
# [e-mail]

# }