Big_LD | R Documentation |
Big_LD
returns the estimation of LD block regions of given data.
Big_LD(geno, SNPinfo, CLQcut = 0.5, clstgap = 40000, leng = 200, subSegmSize = 1500)
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 |
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. |
A data frame of block estimation result. Each row of data frame shows the starting SNP and end SNP of each estimated LD block
Sun-Ah Kim <sunny03@snu.ac.kr>, Yun Joo Yoo <yyoo@snu.ac.kr>
CLQD
, LDblockHeatmap
data(geno) data(SNPinfo) Big_LD(geno, SNPinfo) Big_LD(geno, SNPinfo, CLQcut = 0.5, clstgap = 40000, leng = 200, subSegmSize = 1500)
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