CLQD: partitioning into cliques

In sunnyeesl/BigLD: Big-LD

partitioning into cliques

Description

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

Usage

CLQD(subgeno, subSNPinfo, CLQcut = 0.5, clstgap = 40000,
  CLQmode = c("Density", "Maximal"), codechange = FALSE)

Arguments

subgeno	A data frame or matrix of additive genotype data, each column is additive genotype of each SNP.
subSNPinfo	A data frame or matrix of SNPs information. 1st column is rsID and 2nd column is bp position.
CLQcut	A numeric value of threshold for the correlation value |r|, between 0 to 1.
clstgap	An integer value to specifing the 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
CLQmode	A character string to specify 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.
codechange	If TRUE, choose the cliques after code change procedure.

Value

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

Author(s)

Sun-Ah Kim <[e-mail]>, Yun Joo Yoo <[e-mail]>

Examples

data(geno)
data(SNPinfo)
CLQD(geno,SNPinfo,CLQcut = 0.5, clstgap= 40000, CLQmode = 'Maximal', codechange = FALSE)
CLQD(geno,SNPinfo,CLQcut = 0.5, clstgap= 40000, CLQmode = 'Density', codechange = FALSE)

sunnyeesl/BigLD documentation built on July 11, 2022, 8:01 a.m.