LDMap {synbreed} | R Documentation |
Visualization of pairwise Linkage Disequilibrium (LD) estimates generated by
function pairwiseLD
in a LD heatmap for each chromosome using the
LDheatmap
package (Shin et al, 2006) .
LDMap( LDmat, gpData, chr = NULL, file = NULL, fileFormat = "pdf", onefile = TRUE, ... )
LDmat |
Object of class |
gpData |
Object of class |
chr |
|
file |
Optionally a path to a file where the plot is saved to |
fileFormat |
|
onefile |
|
... |
Further arguments that could be passed to function
|
Note: If you have an LDmat
-object with more than one chromosome and
you like to plot all chromosomes, you need to put an empty line for each
chromosome in your script after the LDMap function!
Hans-Juergen Auinger, Theresa Albrecht and Valentin Wimmer
Shin JH, Blay S, McNeney B, Graham J (2006). LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms. Journal of Statistical Software, 16, Code Snippet 3. URL http://stat-db.stat.sfu.ca: 8080/statgen/research/LDheatmap/.
## Not run: library(synbreedData) data(maize) maizeC <- codeGeno(maize) # LD for chr 1 maizeLD <- pairwiseLD(maizeC, chr = 1, type = "matrix") LDMap(maizeLD, maizeC) ## End(Not run)