PopGenome (version 1.2.6)

F_ST.stats-methods: Fixation Index

Description

A generic function to calculate some F-statistics and nucleotide/haplotype diversities.

Usage

## S3 method for class 'GENOME':
F_ST.stats(
object,
new.populations=FALSE,
subsites=FALSE,
detail=TRUE,
mode="ALL",
only.haplotype.counts=FALSE,
FAST=FALSE
)

## S3 method for class 'GENOME':
get.diversity(object,between=FALSE)
## S3 method for class 'GENOME':
get.F_ST(object,mode=FALSE,pairwise=FALSE)

Arguments

object

An object of class "GENOME"

new.populations

list of populations. default:FALSE

subsites

"transitions": SNPs which are transitions. "transversions": SNPs which are transversions. "syn": synonymous sites. "nonsyn": nonsynonymous sites. "exon": SNPs in exon regions. "i

detail

detail statistics. Note: slower!

between

TRUE: show between diversities. FALSE: show within diversities

mode

mode="haplotype" or mode="nucleotide"

only.haplotype.counts

only calculate the haplotype counts

FAST

if TRUE only calculate a subset of statistics. see details !

pairwise

show paiwise comparisons. default:FALSE

Value

• rlll{ Slot Reference Description 1. haplotype.F_ST [1] Fixation Index based on haplotype frequencies 2. nucleotide.F_ST [1] Fixation Index based on minor.allele frequencies 3. Nei.G_ST [2] Nei's Fixation Index 4. Hudson.G_ST [3] see reference ... 5. Hudson.H_ST [3] see reference ... 6. Hudson.K_ST [3] see reference ... 7. nuc.diversity.within [1] Nucleotide diversity (within the population) 8. hap.diversity.within [1] Haplotype diversity (within the population) 9. Pi [4] Diversity from Nei (within the population) 10. hap.F_ST.vs.all [1] Fixation Index for each population against the rest (haplotype) 11. nuc.F_ST.vs.all [1] Fixation Index for each population against the rest (nucleotide) 12. hap.diversity.between [1] Haplotype diversities between populations 13. nuc.diversity.between [1] Nucleotide diversities between populations 14. nuc.F_ST.pairwise [1] Fixation Index for every pair of population (nucleotide) 15. hap.F_ST.pairwise [1] Fixation Index for every pair of population (haplotype) 16. Nei.G_ST.pairwise [2] Fixation Index for every pair of population (Nei) 17. region.stats an object of class "region.stats" for detail statistics }

Details

If FAST is switched on, this module only calculates nuc.diversity.within, hap.diversity.within, haplotype.F_ST, nucleotide.F_ST and pi. Note: The nucleotide diversity have to be devided by [e-mail]

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. (1973). Analysis of gene diversity in subdivided populations. Proc.Natl. Acad. Sci. USA 70: 3321-3323 [3] Hudson, R. R., Boos, D.D. and N. L. Kaplan (1992). A statistical test for detecting population subdivison. Mol. Biol. Evol. 9: 138-151. [4] Nei, M. (1987). Molecular Evolutionary Genetics. Columbia Univ. Press, New York.

See Also

# methods?F_ST.stats.2 #F_ST.stats.2

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- F_ST.stats(GENOME.class)
# GENOME.class <- F_ST.stats(GENOME.class,list(1:4,5:10),subsites="syn")
# GENOME.class <- F_ST.stats(GENOME.class,list(c("seq1","seq5","seq3"),c("seq2","seq8")))
# show the result:
# get.F_ST(GENOME.class)
# get.F_ST(GENOME.class, pairwise=TRUE)
# get.diversity(GENOME.class, between=TRUE)
# GENOME.class@Pi --> population specific view
# [e-mail]