detail.stats-methods: Several statistics

Description

This generic function calculates some mixed statistics.

Usage

## S3 method for class 'GENOME':
detail.stats(
	object,
	new.populations=FALSE,
	new.outgroup=FALSE,
	subsites=FALSE,
	biallelic.structure=FALSE,
	mismatch.distribution=FALSE,
	site.spectrum=TRUE,
        site.FST=FALSE
        )
## S3 method for class 'GENOME':
get.detail(object, biallelic.structure=FALSE)

Arguments

object

an object of class "GENOME"

new.populations

list of populations.

new.outgroup

outgroup sequences.

subsites

"transitions": SNPs that are transitions. "transversions": SNPs that are transversions. "syn": synonymous sites. "nonsyn": nonsynonymous sites. "exon": SNPs in exon regions. "int

biallelic.structure

fixed and shared polymorphisms (stored in GENOME.class@region.stats).

mismatch.distribution

statistics based on mismatch distribution

site.spectrum

minor allele frequency of each SNP

site.FST

computes FST for each SNP

Value

The return value is a modified object of class "GENOME" ------------------------------------------------------------------ The following Slots will be modified in the "GENOME" object ------------------------------------------------------------------
MDSD...
MDG1...
MDG2...
region.statsthe slot biallelic.structure and minor.allele.freqs will be filled
The function get.detail(GENOME.class, biallelic.structure=TRUE) returns a matrix for each region, where
0population is polymorphic, the remaining individuals are polymorphic
1population is polymorphic, the remaining individuals are monomorphic
2population is monomorphic, the remaining individuals are polymorphic
3population is monomorphic, the remaining individuals are monomorphic with the same value
4population is monomorphic, the remaining individuals are monomorphic with different values

Examples

Run this code

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- set.populations(GENOME.class,list(1:10))
# GENOME.class <- detail.stats(GENOME.class)
# show the result:
# mismatch.values   <- get.detail(GENOME.class)
# bial.struc.values <- get.detail(GENOME.class, biallelic.structure=TRUE)
# GENOME.class@region.stats@biallelic.structure
# GENOME.class@region.stats@biallelic.structure[[1]]

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