write.plink: Prepare data for PLINK

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

Description

Create input files and corresponding script for PLINK (Purcell et al. 2007) to estimate pairwise LD through function pairwiseLD.

Usage

write.plink(
  gp,
  wdir = getwd(),
  prefix = paste(substitute(gp)),
  ld.threshold = 0,
  type = c("data.frame", "matrix"),
  ld.window = 99999
)

Arguments

gp	gpData object with elements geno and map
wdir	character. Directory for PLINK input files
prefix	character. Prefix for PLINK input files.
ld.threshold	numeric. Threshold for the LD used in PLINK.
type	character. Specifies the type of return value for PLINK.
ld.window	numeric. Window size for pairwise differences which will be reported by PLINK (only for use.plink=TRUE; argument --ld-window-kb in PLINK) to thin the output dimensions. Only SNP pairs with a distance < ld.window are reported (default = 99999).

Value

No value returned. Files prefix.map, prefix.ped and prefixPlinkScript.txt are created in the working directory

Author(s)

Valentin Wimmer

References

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.

See Also

pairwiseLD

Examples

## Not run: 
library(synbreedData)
write.plink(maize, type = "data.frame")

## End(Not run)

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