"F_ST.stats"(
object,
new.populations=FALSE,
subsites=FALSE,
detail=TRUE,
mode="ALL",
only.haplotype.counts=FALSE,
FAST=FALSE
)
"get.diversity"(object,between=FALSE)
"get.F_ST"(object,mode=FALSE,pairwise=FALSE)"GENOME"FALSE "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.
TRUE: show between-diversities. FALSE: show within-diversities"haplotype" or mode="nucleotide"TRUE only calculate a subset of statistics. see details!FALSE| 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 |
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. GENOME@n.sites) 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 GENOME.class@region.stats@site.FST.
4) We recommend to use mode="nucleotide" in case you have many unknowns included in your dataset.
[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.
# 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
# GENOME.class@region.stats
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