linkage.stats-methods: Linkage Disequilibrium

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

Linkage Disequilibrium

Description

A generic function to calculate some linkage disequilibrium statistics.

Usage

## S4 method for signature 'GENOME'
linkage.stats(object,new.populations=FALSE,subsites=FALSE,detail=FALSE,
			do.ZnS,do.WALL=TRUE)
## S4 method for signature 'GENOME'
get.linkage(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": nonsynonymous 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
detail	if you want to calculate some detailed statistics. This can be considerably slower! default:FALSE
do.ZnS	calculate ZnS, ZA and ZZ
do.WALL	calculate Wall's B/Q

Details

Note, the pairwise comparisons are computed via combn(n.snps,2).

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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	Slot	Reference	Description
1.	Wall.B	[2]	Wall $B$ statistic (only adjacent positions are considered)
2.	Wall.Q	[2]	Wall $Q$ statistic (only adjacent positions are considered)
3.	Kelly.Z_nS	[3]	Kelly $Z_nS$ statistic (if detail==TRUE)
4.	Rozas.ZA	[1]	Rozas $ZA$ statistic (adjacent positions, if detail==TRUE)
5.	Rozas.ZZ	[1]	Rozas $ZZ$ statistic ($ZZ=ZA-Z_nS$, if detail==TRUE)

References

[1] Rozas, J., M.Gullaud, G.Blandin, and M.Aguade(2001). DNA variation at the rp49 gene region of Drosophila simulans: evolutionary inferences from an unusual haplotype structure. Genetics 158(3),1147-1155

[2] Wall, J.(1999). Recombination and the power of statistical tests of neutrality. Genet Res 74, 65-79

[3] Kelly,J.K. (1997). A test of neutrality based on interlocus associations. Genetics 146: 1197-1206

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class
# GENOME.class <- linkage.stats(GENOME.class)
# GENOME.class <- linkage.stats(GENOME.class,list(1:4,5:10),subsites="syn")
# GENOME.class <- linkage.stats(GENOME.class,list(c("seq1","seq5","seq3"),
# c("seq2","seq8")))
# GENOME.class <- linkage.stats(GENOME.class, detail=TRUE)
# show the result:
# get.linkage(GENOME.class)
# GENOME.class@Wall.B --> population specific view
# [e-mail]

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