snpgdsLDMat {SNPRelate} | R Documentation

## Linkage Disequilibrium (LD) analysis

### Description

Return a LD matrix for SNP pairs.

### Usage

    snpgdsLDMat(gdsobj, sample.id=NULL, snp.id=NULL, slide=250L,
        method=c("composite", "r", "dprime", "corr", "cov"), mat.trim=FALSE,
        num.thread=1L, with.id=TRUE, verbose=TRUE)

### Arguments

`gdsobj` | an object of class `SNPGDSFileClass`, a SNP GDS file
`sample.id` | a vector of sample id specifying selected samples; if NULL, all samples are used
`snp.id` | a vector of snp id specifying selected SNPs; if NULL, all SNPs are used
`slide` | # of SNPs, the size of sliding window; if `slide < 0`, return a full LD matrix; see details
`method` | "composite", "r", "dprime", "corr", "cov", see details
`mat.trim` | if `TRUE`, trim the matrix when `slide > 0`: the function returns a `"num_slide x (n_snp - slide)"` matrix
`num.thread` | the number of (CPU) cores used; if `NA`, detect the number of cores automatically
`with.id` | if `TRUE`, the returned value with `sample.id` and `sample.id`
`verbose` | if TRUE, show information

### Details

Four methods can be used to calculate linkage disequilibrium values: "composite" for LD composite measure, "r" for R coefficient (by EM algorithm assuming HWE, it could be negative), "dprime" for D', and "corr" for correlation coefficient. The method "corr" is equivalent to "composite", when SNP genotypes are coded as: 0 – BB, 1 – AB, 2 – AA.

If `slide <= 0`, the function returns a n-by-n LD matrix where the value of i row and j column is LD of i and j SNPs. If `slide > 0`, it returns a m-by-n LD matrix where n is the number of SNPs, m is the size of sliding window, and the value of i row and j column is LD of j and j+i SNPs.

### Value

Return a list:

`sample.id` | the sample ids used in the analysis
`snp.id` | the SNP ids used in the analysis
`LD` | a matrix of LD values
`slide` | the size of sliding window

### Author(s)

Xiuwen Zheng

### References

Weir B: Inferences about linkage disequilibrium. Biometrics 1979; 35: 235-254.

Weir B: Genetic Data Analysis II. Sunderland, MA: Sinauer Associates, 1996.

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

### See Also

`snpgdsLDpair`, `snpgdsLDpruning`

### Examples

    # open an example dataset (HapMap)
    genofile <- snpgdsOpen(snpgdsExampleFileName())

    # missing proportion and MAF
    ff <- snpgdsSNPRateFreq(genofile)

    # chromosome 15
    snpset <- read.gdsn(index.gdsn(genofile, "snp.id"))[
        ff$MissingRate==0 & ff$MinorFreq>0 &
        read.gdsn(index.gdsn(genofile, "snp.chromosome"))==15]
    length(snpset)

    # LD matrix without sliding window
    ld.noslide <- snpgdsLDMat(genofile, snp.id=snpset, slide=-1, method="composite")
    # plot
    image(t(ld.noslide$LD^2), col=terrain.colors(16))

    # LD matrix with a sliding window
    ld.slide <- snpgdsLDMat(genofile, snp.id=snpset, method="composite")
    # plot
    image(t(ld.slide$LD^2), col=terrain.colors(16))

    # close the genotype file
    snpgdsClose(genofile)

[Package SNPRelate version 1.20.1 Index]