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#!/bin/bash
# This script shows some examples on how to run ProbABEL's palinear
# module for quantitative traits combined with the mmscore option. See
# also the mmscore.R file on how to prepare the phenotype and
# inverse-sigma files.
# Set the name of the directory with the genotype data files
gtdatadir="gtdata"
# Set the path to the executables (palinear/palogist/pacoxph). If you
# installed ProbABEL according to the instructions in the doc/INSTALL
# file, or installed it via your Linux distribution's package manager,
# you can leave this variable empty.
padir="../src/"
# Using text-based dosage genotype files as input
${padir}palinear \
-p mmscore_pheno.PHE \
-i ${gtdatadir}/mmscore_gen.mlinfo \
-d ${gtdatadir}/mmscore_gen.mldose \
--sep="," \
-o mmscore_dose \
--mmscore mmscore_InvSigma_aj.sex.age.dat
# Using filevector (DatABEL) files as dosage genotype input
${padir}palinear \
-p mmscore_pheno.PHE \
-i ${gtdatadir}/mmscore_gen.mlinfo \
-d ${gtdatadir}/mmscore_gen.dose.fvi \
--sep="," \
-o mmscore_dose_fv \
--mmscore mmscore_InvSigma_aj.sex.age.dat
# Using text-based probability files as genotype input
${padir}palinear \
-p mmscore_pheno.PHE \
-i ${gtdatadir}/mmscore_gen.mlinfo \
-d ${gtdatadir}/mmscore_gen.mlprob \
--ngpreds=2 --sep="," \
-o mmscore_prob \
--mmscore mmscore_InvSigma_aj.sex.age.dat
# Using filevector (DatABEL) probability files as genotype input
${padir}palinear \
-p mmscore_pheno.PHE \
-i ${gtdatadir}/mmscore_gen.mlinfo \
-d ${gtdatadir}/mmscore_gen.prob.fvi \
--ngpreds=2 --sep="," \
-o mmscore_prob_fv \
--mmscore mmscore_InvSigma_aj.sex.age.dat
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