PopGenome (version 2.7.2)

jack.knife.transform: Jacknife Transformation

Description

This generic function transforms an existing object of class "GENOME" into another object of class "GENOME", in which each region corresponds to the (JACKNIFE !) window. Each jacknife window will be excluded from the analyses and the calculation will be applied to the union of all other windows.

Usage

# S4 method for GENOME
jack.knife.transform(object, 
	width=7, jump=5, 
	type=1,
	start.pos=FALSE,end.pos=FALSE
	)

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

Value

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

Examples

# NOT RUN {
# GENOME.class      <- readData("...", format="VCF")
# jack.GENOME.class <- jack.knife.transform(GENOME.class,100,100)
# jack.GENOME.class <- neutrality.stats(jack.GENOME.class)
# jack.GENOME.class@Tajima.D
# }