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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="../data/"
# The output file
log "log"
/*
* Read in data from "../data/jvped"
* This declares that there are 9 (no more or less) fields per record.
* Records will be read in until the end of the file is reached.
*/
file datadir+"jvped",id,sire,dam,y,all1_1,all1_2,all2_1,all2_2,af
# Declare which variables have the pedigree information
pedigree id,sire,dam
# af (affected status) is discrete
discrete af
# 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
# y is censored when individual is unaffected (af=1)
censored y where (af="1")
# Define the model
model y=QTL
# Set up the linkage group
link "chromosome 1",mark1,mark2
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