F_ST.stats-methods: Fixation Index

Description Usage Arguments Details Value References See Also Examples

Description

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

Usage

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

## S4 method for signature 'GENOME'
get.diversity(object,between=FALSE)
## S4 method for signature '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

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. [email protected]) 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 [email protected]@site.FST.
4) We recommend to use mode="nucleotide" in case you have many unknowns included in your dataset.

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

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

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# 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)
# [email protected] --> population specific view
# [email protected]

PopGenome documentation built on May 20, 2018, 5:03 p.m.