plink2cape: Convert plink2 files to cape format

In cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

Convert plink2 files to cape format

Description

Convert plink2 files to cape format

Usage

plink2cape(
  ped = "test.ped",
  map = "test.map",
  pheno = "test.pheno",
  out = "out.csv",
  missing_genotype = "0",
  no_fid = FALSE,
  no_parents = FALSE,
  no_sex = FALSE,
  no_pheno = FALSE,
  verbose = FALSE,
  overwrite = FALSE
)

Arguments

ped	full path to the ped file
map	full path to the map file
pheno	full path to the pheno file
out	full path to the output file
missing_genotype	default is "0"
no_fid	boolean, default is FALSE
no_parents	boolean, default is FALSE
no_sex	boolean, default is FALSE
no_pheno	boolean, default is FALSE
verbose	boolean, default is FALSE, gives some happy little progress messages
overwrite	boolean, default is FALSE, will only remove the existing file if this is set to TRUE

Details

For further information about PLINK and its file formats, see https://zzz.bwh.harvard.edu/plink/

Value

A list with two elements: data_obj and geno_obj These objects are formatted for use in cape and must then be separated to use in run_cape.

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.

cape documentation built on May 29, 2024, 5:11 a.m.