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
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.