LDDist {synbreed} | R Documentation |
Visualization of pairwise Linkage Disequilibrium (LD) estimates generated by
function pairwiseLD
versus marker distance. A single plot is
generated for every chromosome.
LDDist( LDdf, chr = NULL, type = "p", breaks = NULL, n = NULL, file = NULL, fileFormat = "pdf", onefile = TRUE, colL = 2, colD = 1, ... )
LDdf |
object of class |
chr |
|
type |
Character string to specify the type of plot. Use |
breaks |
|
n |
|
file |
|
fileFormat |
|
onefile |
|
colL |
The color for the line if |
colD |
The color for the dots in the plot of |
... |
Further arguments for |
Valentin Wimmer, Hans-Juergen Auinger and Theresa Albrecht
For nonlinear regression curve: Hill WG, Weir BS (1988) Variances and covariances of squared linkage disequilibria in finite populations. Theor Popul Biol 33:54-78.
## Not run: library(synbreedData) # maize data example data(maize) maizeC <- codeGeno(maize) # LD for chr 1 maizeLD <- pairwiseLD(maizeC, chr = 1, type = "data.frame") # scatterplot LDDist(maizeLD, type = "p", pch = 19, colD = hsv(alpha = 0.1, v = 0)) # stacked bars with default categories LDDist(maizeLD, type = "bars") # stacked bars with user-defined categories LDDist(maizeLD, type = "bars", breaks = list( dist = c(0, 10, 20, 40, 60, 180), r2 = c(1, 0.6, 0.4, 0.3, 0.1, 0) )) ## End(Not run)