hlaLDMatrix {HIBAG} | R Documentation

## Composite Linkage Disequilibrium in a Region

### Description

To calculate composite linkage disequilibrium (r2) among SNPs within a region.

### Usage

    hlaLDMatrix(geno, loci=NULL, maf=0.01, assembly="auto", draw=TRUE,
        verbose=TRUE)

### Arguments

`geno` | an object of `hlaSNPGenoClass`
`maf` | MAF filter `>= maf`
`loci` | NULL or a character vector, e.g., "A", "B"
`assembly` | the human genome reference: "hg18", "hg19" (default), "hg38"; "auto" refers to "hg19"; "auto-silent" refers to "hg19" without any warning
`draw` | if TRUE, return a ggplot2 object
`verbose` | if TRUE, show information

### Value

Return a ggplot2 object if `draw=TRUE` or a matrix correlation.

### 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.

### Examples

    region <- 500*1000   # basepair
    geno <- hlaGenoSubsetFlank(HapMap_CEU_Geno, "A", region)
    summary(geno)

    hlaLDMatrix(geno, "A")

[Package HIBAG version 1.22.0 Index]