PopGenome (version 2.7.5)

linkage.stats-methods: Linkage Disequilibrium

Description

A generic function to calculate some linkage disequilibrium statistics.

Usage

# S4 method for GENOME
linkage.stats(object,new.populations=FALSE,subsites=FALSE,detail=FALSE,
			do.ZnS,do.WALL=TRUE)
# S4 method for 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

Value

The return value is a modified object of class "GENOME" --------------------------------------------------------- The following slots will be modified in the "GENOME" object ---------------------------------------------------------

	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)

Details

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

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

# NOT RUN {
# 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]

# }