neutrality.stats-methods | R Documentation |
This generic function calculates some neutrality statistics.
## S4 method for signature 'GENOME' neutrality.stats(object,new.populations=FALSE,new.outgroup=FALSE, subsites=FALSE,detail=FALSE, FAST=FALSE, do.R2=FALSE) ## S4 method for signature 'GENOME' get.neutrality(object,theta=FALSE,stats=TRUE)
object |
an object of class |
new.populations |
list of populations. default: |
new.outgroup |
vector of outgroup sequences. default: |
subsites |
|
detail |
default: |
FAST |
Fast computation. only works if there is no outgroup defined. |
do.R2 |
Ramos-Onsins' & Rozas' R2 |
stats |
show the results of each statistic. default: |
theta |
show the theta values. default: |
The return value is a modified object of class "GENOME"
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The following slots will be modified in the "GENOME"
object
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Slot | Reference | Description | |
1. | n.segregating.sites | Total number of segregating sites | |
2. | Tajima.D | [1] | Tajima's' D statistic 1989 |
3. | Fu.Li.F | [3] | Fu & Li's' F* statistic 1993 |
4. | Fu.Li.D | [3] | Fu & Li's D* statistic 1993 |
5. | Fay.Wu.H | [6] | Fay & Wu's H statistic 2000 |
6. | Zeng.E | [7] | Zeng's E statistic 2006 |
7. | Strobeck.S | [5] | Strobeck's 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] | Ramos-Onsins' & 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] | |
[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
# 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 # GENOME.class@region.stats
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