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LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms

Author

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  • Shin, Ji-Hyung
  • Blay, Sigal
  • McNeney, Brad
  • Graham, Jinko

Abstract

We describe the R function LDheatmap() which produces a graphical display, as a heat map, of pairwise linkage disequilibrium measurements between single nucleotide polymorphisms within a genomic region. LDheatmap() uses the grid graphics system, an alternative to the traditional R graphics system. The features of the LDheatmap() function and the use of tools from the grid package to modify heat maps are illustrated by examples.

Suggested Citation

  • Shin, Ji-Hyung & Blay, Sigal & McNeney, Brad & Graham, Jinko, 2006. "LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 16(c03).
    • Handle: RePEc:jss:jstsof:v:016:c03
    DOI: http://hdl.handle.net/10.18637/jss.v016.c03
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    1. Josephine R. Paris & James R. Whiting & Mitchel J. Daniel & Joan Ferrer Obiol & Paul J. Parsons & Mijke J. Zee & Christopher W. Wheat & Kimberly A. Hughes & Bonnie A. Fraser, 2022. "A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Xiao Zhang & Mark Blaxter & Jonathan M. D. Wood & Alan Tracey & Shane McCarthy & Peter Thorpe & Jack G. Rayner & Shangzhe Zhang & Kirstin L. Sikkink & Susan L. Balenger & Nathan W. Bailey, 2024. "Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    3. Juan E. Rosas & Maia Escobar & Sebastián Martínez & Pedro Blanco & Fernando Pérez & Gastón Quero & Lucía Gutiérrez & Victoria Bonnecarrère, 2020. "Epistasis and Quantitative Resistance to Pyricularia oryzae Revealed by GWAS in Advanced Rice Breeding Populations," Agriculture, MDPI, vol. 10(12), pages 1-16, December.
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    5. Chengqi Cui & Yanyang Liu & Yan Liu & Xianghua Cui & Zhiyu Sun & Zhenwei Du & Ke Wu & Xiaolin Jiang & Hongxian Mei & Yongzhan Zheng, 2021. "Genome-wide association study of seed coat color in sesame (Sesamum indicum L.)," PLOS ONE, Public Library of Science, vol. 16(5), pages 1-14, May.
    6. Hideki Yoshida & Ko Hirano & Kenji Yano & Fanmiao Wang & Masaki Mori & Mayuko Kawamura & Eriko Koketsu & Masako Hattori & Reynante Lacsamana Ordonio & Peng Huang & Eiji Yamamoto & Makoto Matsuoka, 2022. "Genome-wide association study identifies a gene responsible for temperature-dependent rice germination," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    7. Li Lin & Xingrui Zhang & Jialin Fan & Jiawei Li & Sichao Ren & Xin Gu & Panpan Li & Meiling Xu & Jingyi Xu & Wenjing Lei & Dongxiao Liu & Qinfu Sun & Guangqin Cai & Qing-Yong Yang & Youping Wang & Jia, 2024. "Natural variation in BnaA07.MKK9 confers resistance to Sclerotinia stem rot in oilseed rape," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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