plot.getLD {trio} | R Documentation |
Plots either the pairwise r^2 or D' values computed by getLD
. 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", squared = TRUE, col = NULL, start = 1, end = NA, xlab = "", ylab = "", cexAxis = 0.8, alpha = 0.1, ciLD = c(0.7, 0.98), cuRecomb = 0.9, ...)
x |
the output of getLD .
|
y |
either "rSquare" (default), "Dprime" , or "gabriel" specifying
the LD values 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.
|
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 .
|
end |
integer or character string specifying the index or the 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. |
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
|
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.
## Not run: # Andrea's data data(mat) out <- getLD(mat, addVarN=TRUE) # Plot r^2 plot(out) # Plot r starting with SNP 24 and ending with SNP 60. plot(out, squared=FALSE, start=24, end=60) # Now the same for D'. plot(out, "Dprime", start=24, end=60) # Now Gabriel's categories starting with SNP ABI.355 # and ending with SNP CRC.45. plot(out, "gabriel", start="ABI.355", end="CRC.45") ## End(Not run)