PopGenome (version 1.2.6)

sliding.window.transform-methods: Sliding Window Transformation.

Description

This generic function transforms the existing object of class "GENOME" in another object of class "GENOME", so that sliding window calculations become possible without loosing the method-capacity of the PopGenome environment.

Usage

## S3 method for class '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

scanning the whole data by concatenating the regions. If FALSE, the regions are scaned seperately

Value

• The function creates an transformed object of class "GENOME"

Examples

# 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]