LDheatmap.highlight {LDheatmap}R Documentation

Highlight a genetic region in the linkage disequilibrium heat map

Description

The function LDheatmap.highlight is used to highlight a specified genetic region in the linkage disequilibrium (LD) heat map drawn with the LDheatmap function.

Usage

LDheatmap.highlight(LDheatmap, i, j, fill = "NA", col = "black", lwd = 1, lty = 1)

Arguments

LDheatmap An object of class "LDheatmap" (returned by the function LDheatmap).
i A numeric value specifying the index of the first SNP to be in the highlighted region.
j A numeric value specifying the index of the last SNP, which must be different from i, to be in the highlighted region.
fill Color to fill the highlighted area with.
col A character string specifying the color of the line segments defining the boundary of highlighted region; see par.
lwd A positive number specifying the width of the boundary segments.
lty Either an integer or a character string specifying the line type of the boundary segments; see par for possible values.

Value

A data frame of the x and y coordinates of points defining the border of the highlighted area.

Note

The function LDheatmap.highlight highlights the cells representing the pairwise LD for the SNPs located between i-th and j-th (inclusive) SNPs in the genomic region of interest. Note that the order of indices has no effect on the plot. For example, LDheatmap.highlight(LDheatmap, i=2, j=4) is the same as LDheatmap.highlight(LDheatmap, i=4, j=2), which highlights the cells representing the pairwise LD for the second, third and fourth SNPs.

Author(s)

Nicholas Lewin-Koh <nikko@hailmail.net>, Ji-hyung Shin <jshinb@sfu.ca>, Sigal Blay <sblay@sfu.ca>

Examples

data(LDheatmapData)
tt <- LDheatmap(HapMap.dat, genetic.distances=distance)
LDheatmap.highlight(tt, 3, 8, col="blue", fill="green", lwd=3)

[Package LDheatmap version 0.2 Index]