plink2cape {cape}

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.