PopGenome (version 1.2.6)

neutrality.stats-methods: Neutrality Statistics

Description

This generic function calculates some neutrality statistics.

Usage

## S3 method for class 'GENOME':
neutrality.stats(object,new.populations=FALSE,new.outgroup=FALSE,
subsites=FALSE,detail=FALSE, FAST=FALSE, do.R2=FALSE)
## S3 method for class 'GENOME':
get.neutrality(object,theta=FALSE,stats=TRUE)

Arguments

object

an object of class "GENOME"

new.populations

list of populations. default:FALSE

new.outgroup

vector of outgroup sequences. 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

default:FALSE, TRUE for some detail statistics. Note:slower!

FAST

Fast computation. only works if there is no outgroup defined.

do.R2

Rozas R2

stats

show the results of each statistic. default:TRUE

theta

show the theta values. default:FALSE

Value

• Returned value is an modified object of class "GENOME" --------------------------------------------------------- Following slots will be modified in the "GENOME" object --------------------------------------------------------- rlll{ Slot Reference Description 1. n.segregating.sites Total number of segregating sites 2. Tajima.D [1] Tajima D statistic 1989 3. Fu.Li.F [3] Fu & Li F* statistic 1993 4. Fu.Li.D [3] Fu & Li D* statistic 1993 5. Fay.Wu.H [6] Fay & Wu H statistic 2000 6. Zeng.E [7] Zeng E statistic 2006 7. Strobeck.S [5] Strobeck S statistic 1987 (if detail==TRUE) 8. Fu.F_S [4] Fu's F$_{S}$ statistic 1997 (if detail==TRUE) 9. Rozas.R_2 [2] Rozas $R_{2}$ statistic 2002 10. theta_Tajima [1] 11. theta_Watterson 12. theta_Fu.Li [3] 13. theta_Achaz.Watterson 14. theta_Achaz.Tajima 15. theta_Fay.Wu [6] 16. theta_Zeng [7] }

References

[1] Tajima, F.(1989) Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics, 123(3): 585-595. [2] Ramos-Onsins, S.E. and J.Rozas (2002). Statistical Properties of New Neutrality Tests Against Population Growth. Mol.Biol.Evol.19(12),2092-2100 [3] Fu, Y.X. and W.H.Li (1993). Statistical Tests of Neutrality of Mutations. Genetics 133(3),693-709 [4] Fu, Y.-X.(1997). Statistical Tests of Neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147(2),915-925. [5] Strobeck, C. (1987). Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision. Genetics 117, 149-153 [6] Fay, J.C. and C.-I. Wu (2000). Hitchhiking under positive Darwinian selection. Genetics 155 (3),1405-1413 [7] Zeng, K., Y.-X. Fu, S. Shi, and C.-I. Wu (2006). Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174, 1431-1439

Examples

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