PopGenome (version 2.7.5)

sliding.window.transform-methods: Sliding Window Transformation

Description

This generic function transforms an existing object of class "GENOME" into another object of class "GENOME", in which each region corresponds to one window. This allows to apply the full spectrum of PopGenome methods to sliding window data.

Usage

# S4 method for GENOME
sliding.window.transform(object, 
	width=7, jump=5, 
	type=1,
	start.pos=FALSE,end.pos=FALSE,
	whole.data=TRUE
	)

Arguments

object

an object of class "GENOME"

width

window size. default:7

jump

jump size. default:5

type

1 scan only biallelic positions (SNPs), 2 scan the genome. default:1

start.pos

start position

end.pos

end position

whole.data

scan the complete data by concatenating the regions in "object". If FALSE, each region is scanned seperately.

Value

The function creates a transformed object of class "GENOME".

Examples

# NOT RUN {
# GENOME.class       <- readData("...\Alignments")
# slide.GENOME.class <- sliding.window.transform(GENOME.class)
# slide.GENOME.class <- sliding.window.transform(GENOME.class,100,100)
# slide.GENOME.class <- neutrality.stats(slide.GENOME.class)
# [e-mail]
# values             <- get.neutrality(slide.GENOME.class)
# GENOME.class       <- readSNP("Arabidopsis", CHR=1)
# GENOME.slide       <- sliding.window.transform(GENOME.split, 10000, 10000, type=2,
# start.pos=10000000, end.pos=12000000)
# [e-mail]
# }