Ldheatmap manual

 · The function LDheatmap() takes an input data set that provides information on pairwise LD between SNPs in a genomic region, plots color-coded values of the pairwise LD measurements, and returns an object of class “LDheatmap” containing a number of components. LDheatmap() is used to produce a graphical display, as a heat map, of pairwise linkage disequilibrium (LD) measurements for SNPs. The heat map is a false color image in the upper-left diagonal of a square plot. Optionally, a line parallel to the diagonal of the image indicating the physical or genetic map positions of the SNPs may be added, along with text reporting the . LDheatmap LDheatmap() is used to produce a graphical display, as a heat map, of pairwise linkage disequilibrium (LD) measurements for SNPs. The heat map is a false color image in the upper-left diagonal of a square plot.

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 www.doorway.rumap() 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. LDheatmap() uses the grid graphics system, an alterna- tive 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. Keywords: single nucleotide polymorphisms, linkage disequilibrium, grid graphics. 1. Haploview was developed in and is maintained by Mark Daly's lab at the Broad Institute by Jeffrey Barrett, David Bender, Julian Maller, and Jesse Whitworth. The design of the LD and haplotype interfaces is the work of Ben Fry at the MIT MediaLab. Thanks to Andrew Kirby and Hin-Tak Leung for code contributions.

LDheatmap() is used to produce a graphical display, as a heat map, of pairwise linkage disequilibrium (LD) measurements for SNPs. The heat map is a false color image in the upper-left diagonal of a square plot. LDheatmap LDheatmap() is used to produce a graphical display, as a heat map, of pairwise linkage disequilibrium (LD) measurements for SNPs. The heat map is a false color image in the upper-left diagonal of a square plot. Package ‘LDheatmap’ October 8, Version Date Title Graphical Display of Pairwise Linkage Disequilibria Between SNPs Maintainer Brad McNeney.