linkage.stats-methods: Linkage Disequilibrium

Description Usage Arguments Details Value References Examples

Description

A generic function to calculate some linkage disequilibrium statistics.

Usage

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## 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

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# 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)
# [email protected] --> population specific view
# [email protected]

PopGenome documentation built on May 20, 2018, 5:03 p.m.