hlaGenoLD: Composite Linkage Disequilibrium

In zhengxwen/HIBAG: HLA Genotype Imputation with Attribute Bagging

Composite Linkage Disequilibrium

Description

To calculate composite linkage disequilibrium (r2) between HLA locus and SNP markers.

Usage

hlaGenoLD(hla, geno)

Arguments

hla	an object of hlaAlleleClass
geno	an object of hlaSNPGenoClass, or a vector or matrix for SNP data

Value

Return a vector of linkage disequilibrium (r2) for each SNP marker.

Author(s)

Xiuwen Zheng

References

Weir BS, Cockerham CC: Complete characterization of disequilibrium at two loci; in Feldman MW (ed): Mathematical Evolutionary Theory. Princeton, NJ: Princeton University Press, 1989.

Zaykin, D. V., Pudovkin, A., and Weir, B. S. (2008). Correlation-based inference for linkage disequilibrium with multiple alleles. Genetics 180, 533-545.

Examples

# plot linkage disequilibrium
ymax <- 0.16
plot(NaN, NaN, xlab="SNP Position (in KB)",
    ylab="Composite Linkage Disequilibrium (r2)",
    xlim=range(HapMap_CEU_Geno$snp.position)/1000, ylim=c(0, ymax),
    main="Major Histocompatibility Complex")

hla.list <- c("A", "C", "DQA1")
col.list <- 1:3

# for-loop
for (i in 1:3)
{
    hla.id <- hla.list[i]

    # make a "hlaAlleleClass" object
    hla <- hlaAllele(HLA_Type_Table$sample.id,
        H1 = HLA_Type_Table[, paste(hla.id, ".1", sep="")],
        H2 = HLA_Type_Table[, paste(hla.id, ".2", sep="")],
        locus=hla.id, assembly="hg19")

    # linkage disequilibrium between HLA locus and SNP markers
    ld <- hlaGenoLD(hla, HapMap_CEU_Geno)

    # draw
    points(HapMap_CEU_Geno$snp.position/1000, ld, pch="*", col=i)
    x <- (hla$pos.start/1000 + hla$pos.end/1000)/2
    abline(v=x, col=col.list[i], lty=3, lwd=2.5)
    points(x, ymax, pch=25, col=7, bg=col.list[i], cex=1.5)
}
legend("topleft", col=col.list, pt.bg=col.list, text.col=col.list, pch=25,
    legend=paste("HLA -", hla.list))

zhengxwen/HIBAG documentation built on Nov. 19, 2024, 1:01 p.m.