Big_LD: Estimation of LD block regions

In sunnyeesl/BigLD: Big-LD

Estimation of LD block regions

Description

Big_LD returns the estimation of LD block regions of given data.

Usage

Big_LD(geno, SNPinfo, CLQcut = 0.5, clstgap = 40000, leng = 200,
  subSegmSize = 1500)

Arguments

geno	A data frame or matrix of additive genotype data, each column is additive genotype of each SNP.
SNPinfo	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
leng	An integer value to specify the number of SNPs in a preceding and a following region of each sub-region boundary, every SNP in a preceding and every SNP in a following region need to be in weak LD.
subSegmSize	An integer value to specify the upper bound of the number of SNPs in a one-take sub-region.

Value

A data frame of block estimation result. Each row of data frame shows the starting SNP and end SNP of each estimated LD block

Author(s)

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

See Also

CLQD, LDblockHeatmap

Examples

data(geno)
data(SNPinfo)
Big_LD(geno, SNPinfo)
Big_LD(geno, SNPinfo, CLQcut = 0.5, clstgap = 40000, leng = 200, subSegmSize = 1500)

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