CLQD {gpart} | R Documentation

## partitioning into cliques

### Description

`CLQD` partitioning the given data into subgroups that contain SNPs which are highly correlated.

### Usage

    CLQD(geno, SNPinfo, CLQcut=0.5, clstgap=40000,
    hrstType=c("near-nonhrst", "fast", "nonhrst"), hrstParam=200,
    CLQmode=c("density", "maximal"), LD=c("r2", "Dprime"))

### Arguments

`geno` | Data frame or matrix of additive genotype data, each column is additive genotype of each SNP. (Use data of non-monomorphic SNPs)
`SNPinfo` | Data frame or matrix of SNPs information. 1st column is rsID and 2nd column is bp position.
`CLQcut` | Numeric constant; a threshold for the LD measure value |r|, between 0 to 1. Default 0.5.
`clstgap` | Numeric constant; a threshold of physical distance (bp) between two consecutive SNPs which do not belong to the same clique, i.e., if a physical distance between two consecutive SNPs in a clique greater than `clstgap`, then the algorithm split the cliques satisfying each clique do not contain such consecutive SNPs. Default 40000.
`hrstType` | Character constant; heuristic methods. If you want to do not use heuristic algorithm, set `hrstType = "nonhrst"`. If you want to use heuristic algorithm suggested in Kim et al.,(2017), set `hrstType = "fast"`. That algorithm is fastest heuristic algorithm and suitable when your memory capacity is not greater than 8GB. If you want to obtain the results similar to the that of non-heuristic algorithm, set `hrstType = "near-nonhrst"`.
`hrstParam` | Numeric constant; parameter for heuristic algorithm "near-nonhrst". Default is `200`. It is recommended that you set the parameter to greater than 150.
`CLQmode` | Character constant; the way to give priority among detected cliques. if `CLQmode = "density"` then the algorithm gives priority to the clique of largest value of (Number of SNPs)/(range of clique), else if `CLQmode = "maximal"`, then the algorithm gives priority to the largest clique. The default is "density".
`LD` | Character constant; LD measure to use, "r2" or "Dprime". Default "r2".

### Value

A vector of cluster numbers of all SNPs (`NA` represents singleton cluster).

### Author(s)

Sun-Ah Kim <sunny03@snu.ac.kr>, Yun Joo Yoo <yyoo@snu.ac.kr>

### See Also

`BigLD`

### Examples

    data(geno)
    data(SNPinfo)
    CLQD(geno=geno[,1:100],SNPinfo=SNPinfo[100,])
    CLQD(geno=geno[,1:100],SNPinfo=SNPinfo[100,], CLQmode = 'maximal')
    CLQD(geno=geno[,1:100],SNPinfo=SNPinfo[100,], LD='Dprime')

[Package gpart version 1.0.3 Index]