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# Declare "*" as the symbol for a missing record
missing "*"
# It can be convenient to put directory names into variables so they can be easily changed.
datadir=""
# The output file
log "log"
/*
* Read in data from "../data/jvped1"
* The [RS="\n"] clause tells the program that records are separated by
* newline characters (\n). This allows the handling of short lines, as
* are found in jvped1.
*/
file [RS="\n"] datadir+"jvped1",id,sire,dam,y,all1_1,all1_2,all2_1,all2_2
# Declare which variables have the pedigree information
pedigree id,sire,dam
# Link the observed haplotypes to markers
marker locus mark1[all1_1,all1_2],mark2[all2_1,all2_2]
# We have a trait locus (actually this can be multiple trait loci)
trait locus QTL
# Define the model
model y=QTL+id
# Set up the linkage group
link "chromosome 1",mark1,mark2
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