Hi,

I have few plink ped files with me.

The file format:

Family ID, Individual ID, Paternal ID, Maternal ID, sex, Phenotype

I am trying to perform linkage analysis in R using the "paramlink" package by Magnus Dehli Vigeland.

My data is in the format,

HCC1187  GS00258-DNA_E01  0 0  1  2
HCC1187  GS00258-DNA_F01  0 0  2  1
HCC1187  GS00258-DNA_A03  GS00258-DNA-E01  GS00258-DNA-F01   1 2
HCC1187  GS00258-DNA_B03  GS00258-DNA-E01  GS00258-DNA-F01   2 1

I am trying to read my ped file into R for use in paramlink package. I am able to read the files normally as,

hcc1187 <- read.delim("hcc1187.ped", header=FALSE, comment.char="#")

But when I try to import it as,

hcc1187 <- linkdat("hcc1187.ped")

I encounter errors such as,

Error in linkdat("hcc1187.ped") : Pedigree columns must be numeric.
In addition: Warning message:
In linkdat("hcc1187.ped") : NAs introduced by coercion

How should I import the ped files for use for paramlink package.

Thanks in advance.