detail.stats-methods: Several statistics

Description Usage Arguments Value Examples

Description

This generic function calculates some mixed statistics.

Usage

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## S4 method for signature 'GENOME'
detail.stats(
	object,
	new.populations=FALSE,
	new.outgroup=FALSE,
	subsites=FALSE,
	biallelic.structure=FALSE,
	mismatch.distribution=FALSE,
	site.spectrum=TRUE,
        site.FST=FALSE
        )
## S4 method for signature '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.
"intron": SNPs in intron regions.
"coding": SNPs in coding regions (CDS).
"utr": SNPs in UTR regions.
"gene": SNPs in genes.

biallelic.structure

fixed and shared polymorphisms (stored in [email protected]).

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.stats

the 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

0

population is polymorphic, the remaining individuals are polymorphic


1

population is polymorphic, the remaining individuals are monomorphic


2

population is monomorphic, the remaining individuals are polymorphic


3

population is monomorphic, the remaining individuals are monomorphic with the same value


4

population is monomorphic, the remaining individuals are monomorphic with different values


Examples

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# 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)
# [email protected]@biallelic.structure
# [email protected]@biallelic.structure[[1]]
 

PopGenome documentation built on May 20, 2018, 5:03 p.m.