PopGenome (version 1.2.6)

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
        )
## 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 which are transitions. "transversions": SNPs which are transversions. "syn": synonymous sites. "nonsyn": nonsynonymous sites. "exon": SNPs in exon regions. "i

biallelic.structure

fixed and shared polymorphisms (stored in [e-mail]).

mismatch.distribution

statistics based on mismatch distribution

site.spectrum

minor-allele frequency of each SNP

Value

• returned value is an modified object of class "GENOME" -------------------------------------------------------------- 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
  pop is polymorph rest is polymorph
• 1
  pop is polymorph rest is monomorph
• 2
  pop is monomorph rest is polymorph
• 3
  pop is monomorph rest is monomorph with same value
• 4
  pop is monomorph rest is monomorph with different values

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- detail.stats(GENOME.class)
# GENOME.class <- detail.stats(GENOME.class,list(1:7,8:12))
# show the result:
# mismatch.values   <- get.detail(GENOME.class)
# bial.struc.values <- get.detail(GENOME.class, biallelic.structure=TRUE)
# [e-mail]@biallelic.structure
# [e-mail]@biallelic.structure[[1]]