sweeps.stats-methods: Selective Sweeps

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

Selective Sweeps

Description

This module calculates some statistics to detect selective sweeps.

Usage

## S4 method for signature 'GENOME'
sweeps.stats(object,new.populations=FALSE,subsites=FALSE,
 freq.table=FALSE, FST=FALSE)
## S4 method for signature 'GENOME'
get.sweeps(object)

Arguments

object	an object of class "GENOME"
new.populations	list of populations. default:FALSE
subsites	"transitions": SNPs that are transitions. "transversions": SNPs that are transversions. "syn": synonymous sites. "nonsyn": non-synonymous sites. "exon": SNPs in exon regions. "intron": SNPs in intron regions. "coding": SNPs in coding regions (CDS). "utr": SNPs in UTR regions. "gene": SNPs in genes. default:FALSE
freq.table	the frequency counts for the CLR test. "list"
FST	use FST values instead of the minor allele frequencies

Details

The freq.table contains the global sets of frequency counts. It can be produced with the module detail.stats. The values in the slot [e-mail]@minor.allele.frequencies can be used to create this global set. (use the R function table) freq.table is a list of length n.pops.

Value

The return value is a modified object of class "GENOME"

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The following slots will be modified in the "GENOME" object
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CL	Composite Likelihood of SNPs
CLR	Nielsen's CLR test

References

Cai JJ (2008) PGEToolbox: A Matlab toolbox for population genetics and evolution Journal of Heredity Jul-Aug;99(4):438-40.doi:10.1093/jhered/esm127

Nielson, R. (2005). Genomic scans for selective sweeps using SNP data Genome Res. 2005 15: 1566-1575

Examples

# Reading one alignment stored in the folder Aln
# GENOME.class <- readData("\home\Aln")
#
# CL
# GENOME.class <- sweeps.stats(GENOME.class)
# GENOME.class@CL
#
# CLR
# create global set
# GENOME.class  <- detail.stats(GENOME.class)
# freq <- [e-mail]@minor.allele.freqs[[1]]
# freq.table <- list()
# freq.table[[1]] <- table(freq)
# define the region of interest
# GENOME.class.split <- splitting.data(GENOME.class, positions= ...)
# calculate CLR
# GENOME.class.split <- sweeps.stats(GENOME.class.split, freq.table=freq.table)
# GENOME.class@CLR
 

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