LDMap: LD Heatmap

In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description

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) .

Usage

LDMap(
  LDmat,
  gpData,
  chr = NULL,
  file = NULL,
  fileFormat = "pdf",
  onefile = TRUE,
  ...
)

Arguments

LDmat	Object of class LDmat generated by function pairwiseLD and argument type="matrix"
gpData	Object of class gpData that was used in pairwiseLD
chr	numeric. Return value is a plot for each chromosome in chr.
file	Optionally a path to a file where the plot is saved to
fileFormat	character. At the moment two file formats are supported: pdf and png. Default is "pdf".
onefile	logical. If fileFormat = "pdf" you can decide, if you like to have all graphics in one file or in multiple files.
...	Further arguments that could be passed to function LDheatmap

Details

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!

Author(s)

Hans-Juergen Auinger, Theresa Albrecht and Valentin Wimmer

References

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/.

See Also

pairwiseLD, LDheatmap, LDDist

Examples

## 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)

synbreed documentation built on March 12, 2021, 3:01 a.m.