sliding.window.transform-methods: Sliding Window Transformation

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

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 signature '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".

Note

If you want to scan regions seperately (whole.data=FALSE), you may not use the big.data option in the readData function. PopGenome will scan the data from position 1 to the last observed SNP if start or end-positions are not specified.

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]

Example output

Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="/work/tmp/tmp/RtmpDYvsc2"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

The following objects are masked from 'package:bit':

    clone, clone.default, clone.list

The following objects are masked from 'package:utils':

    write.csv, write.csv2

The following objects are masked from 'package:base':

    is.factor, is.ordered

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.