plot.LDblocks {trio} | R Documentation |
Plots either the pairwise D' values or the pairwise LD categorization used in the procedure of Gabriel et al. (2002). Additionally, the LD blocks are marked in this plot.
## S3 method for class 'LDblocks' plot(x, y = "gabriel", col = NULL, start = 1, end = NA, xlab = "", ylab = "", cexAxis = 0.8, block.col = 2, block.lwd = 3, ...)
x |
the output of |
y |
either |
col |
a vector specifying the colors used in plotting of the LD values. If |
start |
integer or character string specifying the index or 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 name of the last SNP, respectively, that should be plotted. |
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. |
block.col |
the color of the lines used to show the borders of the LD blocks. |
block.lwd |
numeric value specifying the size of the lines used to show the borders of the LD blocks |
... |
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) # Estimate LD blocks. blocks <- findLDblocks(LDdata) # Alternatively, the LD blocks can be estimated by ld.out <- getLD(LDdata, addVarN=TRUE) blocks2 <- findLDblocks(ld.out) # Plot the LD blocks showing the Gabriel categorization. plot(blocks) # Plot the LD blocks showing the Dprime values. plot(blocks, "Dprime")