trio (version 3.10.0)

plot.getLD: Plotting a getLD or getLDlarge Object

Description

Plots either the pairwise r^2 or D' values computed by either getLD or getLDlarge. Can also be used to plot the categorizations used in the procedure of Gabriel et al. (2002).

Usage

"plot"(x, y = "rSquare", start = 1, end = NA, squared = TRUE, col = NULL, xlab = "", ylab = "", cexAxis = 0.8, alpha = 0.1, ciLD = c(0.7, 0.98), cuRecomb = 0.9, ...) 
"plot"(x, y = "rSquare", start = NA, end = NA, squared = TRUE,  col = NULL, xlab = "", ylab = "", cexAxis = 0.8, alpha = 0.1,  ciLD = c(0.7,0.98), cuRecomb = 0.9, ...)

Arguments

x

the output of getLD or getLDlarge.

y

either "rSquare" (default), "Dprime", or "gabriel" specifying the LD values that should be plotted.

start

integer or character string specifying the index or the name of the first SNP, respectively, that should be plotted, where the index corresponds to the column (or row if snp.in.col = FALSE) in the matrix used as input in getLD or getLDlarge.

end

integer or character string specifying the index or the name of the last SNP, respectively, that should be plotted.

squared

should the $r^2$ values be plotted? If FALSE, the $r$ values are plotted. Only considered if y = "rSquare".

col

a vector specifying the colors used in plotting of the LD values. If y = "rSquare" or y = "Dprime", different levels of gray will be used by default (the darker, the higher is the LD value). If y = "gabriel", strong LD is by default marked by blue fields, evidence of recombination by white color, and others by yellow.

xlab

character string naming the label of the x-axis.

ylab

character string naming the label of the y-axis.

cexAxis

a numeric value specifying the relative size of the SNP names displayed at the axes of the plot.

alpha

numeric value between 0 and 1. Only considered if y = "gabriel". For each pair of SNPs, a two-sided 100 * (1 - alpha)% confidence interval of D' is computed, and used to specify pairs of SNPs that are either in strong LD, or show historical evidence of recombination (see ciLD and cuRecomb). All SNP pairs not falling into these two categories are specified as 'Others'.

ciLD

numeric vector consisting of two values between 0 and 1. Only considered if y = "gabriel". If the lower bound of the confidence interval of D' for a SNP pair is larger than or equal to the first value in ciLD and the upper bound is larger than or equal to the second value, then this pair of SNP is considered to be in strong LD.

cuRecomb

numeric value between 0 and 1. Only considered if y = "gabriel". If the upper bound of the confidence interval of D' for a SNP pair is smaller than cuRecomb, then this pair of SNP is considered to show evidence of recombination.

...

further arguments of image

References

Gabriel, S.B. et al. (2002). The Structure of Haplotype Blocks in the Human Genome. Science, 296, 2225-2229.

See Also

getLD, plot.LDblocks

Examples

# Load the simulated data.
data(trio.data)

# The values of Dprime and Rsquare for each pair of SNPs 
# in LDdata can be computed by
ld.out <- getLD(LDdata)

# By default, the LD measures are returned as a vector.
# If they should be returned as a matrix, then use
ld.out2 <- getLD(LDdata, asMatrix = TRUE)

# The matrix of the Rsquare values can be plotted by
plot(ld.out)

# The matrix of the Dprime values can be plotted by
plot(ld.out, "Dprime")