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Haplotype Analysis

GB Gehendra Bhattarai
AS Ainong Shi
CF Chunda Feng
BD Braham Dhillon
BM Beiquan Mou
JC James C. Correll
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Haplotype block analysis was performed within the associated region obtained from the whole panel in the Haploview 4.2 (Barrett et al., 2005). The haplotype blocks were defined using the confidence interval method of Gabriel et al. (2002), and a pairwise measure of LD (r2) was plotted as a heatmap. Haplotype analysis was further performed in the Plink v1.07 (Purcell et al., 2007) using default settings. The haplotype alleles from the haplotype blocks were utilized as multiallelic markers to conduct haplotype-based association analysis using the logistic regression and linear regression models in Plink v1.07.

Copyright and License information:  ©2020 Bhattarai, Shi, Feng, Dhillon, Mou and Correll.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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