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|
#!/bin/bash
# This script shows some examples on how to run ProbABEL's palinear
# module for quantitative 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="${padir}"
# Using text-based dosage genotype files as input
echo "basic analysis"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.mldose \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 \
-o height_base
# Using filevector (DatABEL) files as dosage genotype input
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.dose.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 \
-o height_base_fv
echo "Option --allcov"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.dose.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --allcov \
-o height_allcov_fv
echo "Option --interaction=1"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.dose.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --interaction=1 \
-o height_int1_fv
echo "Option --robust"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.dose.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --robust \
-o height_robust_fv
echo "Option --robust --interaction=1"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.dose.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --robust --interaction=1 \
-o height_robust_int1_fv
# Using text-based probability files as genotype input
echo "Option --ngp=2, mlprob file"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.mlprob \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --ngp=2 \
-o height_ngp2
# Using filevector (DatABEL) probability files as genotype input
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.prob.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --ngp=2 \
-o height_ngp2_fv
echo "Option --ngp=2 --allcov"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.prob.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --ngp=2 --allcov \
-o height_ngp2_allcov_fv
echo "Option --ngp=2 --interaction=1"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.prob.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --ngp=2 --interaction=1 \
-o height_ngp2_int1_fv
echo "Option --ngp=2 --robust"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.prob.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --ngp=2 --robust \
-o height_ngp2_robust_fv
echo "Option --ngp=2 --robust --interaction=1"
${padir}palinear \
-p height.txt \
-d ${gtdatadir}/test.prob.fvi \
-i ${gtdatadir}/test.mlinfo \
-m ${gtdatadir}/test.map \
-c 19 --ngp=2 --robust --interaction=1 \
-o height_ngp2_robust_int1_fv
|
