PopGenome (version 2.7.2)

F_ST.stats-methods: Fixation Index

Description

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

Usage

# S4 method for GENOME
F_ST.stats(
object,
new.populations=FALSE,
subsites=FALSE,
detail=TRUE,
mode="ALL",
only.haplotype.counts=FALSE,
FAST=FALSE
)
# S4 method for GENOME
get.diversity(object,between=FALSE)
# S4 method for 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 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.

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

	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	[1,5]	Nucleotide diversity (within the population)
8.	hap.diversity.within	[1]	Haplotype diversity (within the population)
9.	Pi	[4]	Nei's diversity (within the population)
10.	hap.F_ST.vs.all	[1]	Fixation Index for each population against all other individuals (haplotype)
11.	nuc.F_ST.vs.all	[1]	Fixation Index for each population against tall other individuals (nucleotide)
12.	hap.diversity.between	[1]	Haplotype diversities between populations
13.	nuc.diversity.between	[1,5]	Nucleotide diversities between populations
14.	nuc.F_ST.pairwise	[1]	Fixation Index for every pair of populations (nucleotide)
15.	hap.F_ST.pairwise	[1]	Fixation Index for every pair of populations (haplotype)
16.	Nei.G_ST.pairwise	[2]	Fixation Index for every pair of populations (Nei)
17.	region.stats		an object of class "region.stats" for detailed 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: 1) The nucleotide diversities have to be devided by the size of region considered (e.g. [e-mail]) to give diversities per site. 2) When missing or unknown nucleotides are included (include.unknown=TRUE) those sites are completely deleted in case of haplotype based statistics. 3) The function detail.stats(...,site.FST=TRUE) will compute SNP specific FST values which are then stored in the slot [e-mail]@site.FST. 4) We recommend to use mode="nucleotide" in case you have many unknowns included in your dataset.

References

[1] Hudson, R. R., M. Slatkin, and W.P. Maddison (1992). Estimating 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. [5] Wakeley, J. (1996).The Variance of Pairwise Nucleotide Differences in Two Populations with Migration. THEORETICAL POPULATION BIOLOGY. 49, 39-57.

See Also

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

Examples

# NOT RUN {
# 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]

# }