write.ped {hierfstat}

Write ped file for analyses with PLINK

Description

write a ped and a map file suitable for analysis with PLINK

Usage

write.ped(dat, ilab = NULL, pop = NULL, 
        fname = "dat",na.str="0",f.id=NULL,m.id=NULL,loc.pos=NULL,sex=NULL)

Arguments

dat

a hierfstat data frame. if pop=NULL, the first column should contain the population identifier, otherwise it contains genotypes at the first locus

ilab

individual labels

pop

population id

fname

filename for ped file

na.str

character string to use for missing values

f.id

father id. default to unknown

m.id

mother id. default to unknown

loc.pos

the loci position default to unknown

sex

the individual sex. default to unknown

Value

a map file containing the loci positions

a ped file containing genotypes etc...

References

Chang et al. (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets