plot.getLD {trio} | R Documentation |
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).
## S3 method for class 'getLD' 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, ...) ## S3 method for class 'getLDlarge' 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, ...)
x |
the output of |
y |
either |
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 |
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 |
col |
a vector specifying the colors used in plotting of the LD values. If |
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 |
ciLD |
numeric vector consisting of two values between 0 and 1.
Only considered if |
cuRecomb |
numeric value between 0 and 1. Only considered if |
... |
further arguments of |
Holger Schwender, holger.schwender@udo.edu
Gabriel, S.B. et al. (2002). The Structure of Haplotype Blocks in the Human Genome. Science, 296, 2225-2229.
# 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")