Achaz.stats: Achaz statistic

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

Description

Achaz statistic

Usage

## S4 method for signature 'GENOME'
Achaz.stats(object,new.populations=FALSE,new.outgroup=FALSE,subsites=FALSE)

Arguments

object	an object of class "GENOME"
new.populations	list of populations. default:FALSE
new.outgroup	outgroup vector. 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. default:FALSE

Value

returned value is a modified object of class "GENOME"

————————————————————–
The following Slots will be modified in the "GENOME" object
————————————————————–

Yach	Achaz Y statistic

References

Achaz G.,2008 Testing for neutrality in samples with sequencing errors. Genetics 179: 1409.

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- Achaz.stats(GENOME.class)
# GENOME.class <- Achaz.stats(GENOME.class,list(1:7,8:12))
# show the result:
# GENOME.class@Yach
 

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