F_ST.stats.2-methods: Fixation Index (2)

In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description

A generic function to calculate some FST measurenments.

Usage

## S4 method for signature 'GENOME'
F_ST.stats.2(object,new.populations="list",subsites=FALSE,snn=TRUE,Phi_ST=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.
snn	Snn statistic from Hudson
Phi_ST	Statistic from Excoffier et al.

Value

Returned value is an modified object of class "GENOME"

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Following slots will be modified in the "GENOME" object
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	Slot	Reference	Description
1.	Hudson.Snn	[1]	Snn statistic from Hudson (2000)
2.	Phi_ST	[2]	Phi_ST from Excoffier (1992)

References

[1] Hudson, R. R. (2000).A new statistic for detecting genetic differentiation. Genetics 155: 2011-2014.

[2] Excoffier, L., Smouse, P., Quattro, J. (1992),Analysis of molecular variance inferred from met-
ric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.
Genetics 131: 479-91

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- F_ST.stats.2(GENOME.class)
# GENOME.class <- F_ST.stats.2(GENOME.class,list(1:4,5:10))
# GENOME.class <- F_ST.stats.2(GENOME.class,
# list(c("seq1","seq5","seq3"),c("seq2","seq8")))
# show the result:
# [e-mail]

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.