hlaGenoLD {HIBAG} | R Documentation

## 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))

[Package HIBAG version 1.24.0 Index]