jack.knife.transform-methods: Jacknife Transformation

In pievos101/PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

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 signature '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".

Note

This function currently is only available for SNP data formats. PopGenome will scan the data from position 1 to the last observed SNP if start or end-positions are not specified. This mechanism can also be applied to the splitting.data() function. Just set [e-mail] <- TRUE after splitting the data.

Examples

# 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

pievos101/PopGenome documentation built on Feb. 24, 2023, 7:11 a.m.