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#!/bin/bash
# This script shows some examples on how to run ProbABEL's palogist
# module for binary traits.
# 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}palogist \
-p logist_data.txt \
-d ${gtdatadir}/test.mldose \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 \
-o logist
# Using filevector (DatABEL) files as dosage genotype input
${padir}palogist \
-p logist_data.txt \
-d ${gtdatadir}/test.dose.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 \
-o logist_fv
# Using text-based probability files as genotype input
${padir}palogist \
-p logist_data.txt \
-d ${gtdatadir}/test.mlprob \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
--ngpreds=2 \
-c 19 \
-o logist_prob
# Using filevector (DatABEL) probability files as genotype input
${padir}palogist \
-p logist_data.txt \
-d ${gtdatadir}/test.prob.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
--ngpreds=2 \
-c 19 \
-o logist_prob_fv
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