[Genabel-commits] r1314 - in pkg/ProbABEL/examples: . gtdata
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Aug 25 22:13:23 CEST 2013
Author: lckarssen
Date: 2013-08-25 22:13:23 +0200 (Sun, 25 Aug 2013)
New Revision: 1314
Added:
pkg/ProbABEL/examples/example_bt.sh
pkg/ProbABEL/examples/example_cox.sh
pkg/ProbABEL/examples/example_mmscore.sh
pkg/ProbABEL/examples/example_qt.sh
pkg/ProbABEL/examples/gtdata/
pkg/ProbABEL/examples/gtdata/mmscore_gen.dose.fvd
pkg/ProbABEL/examples/gtdata/mmscore_gen.dose.fvi
pkg/ProbABEL/examples/gtdata/mmscore_gen.mldose
pkg/ProbABEL/examples/gtdata/mmscore_gen.mlinfo
pkg/ProbABEL/examples/gtdata/mmscore_gen.mlprob
pkg/ProbABEL/examples/gtdata/mmscore_gen.prob.fvd
pkg/ProbABEL/examples/gtdata/mmscore_gen.prob.fvi
pkg/ProbABEL/examples/gtdata/test.dose.fvd
pkg/ProbABEL/examples/gtdata/test.dose.fvi
pkg/ProbABEL/examples/gtdata/test.map
pkg/ProbABEL/examples/gtdata/test.mldose
pkg/ProbABEL/examples/gtdata/test.mlinfo
pkg/ProbABEL/examples/gtdata/test.mlprob
pkg/ProbABEL/examples/gtdata/test.prob.fvd
pkg/ProbABEL/examples/gtdata/test.prob.fvi
pkg/ProbABEL/examples/height.txt
pkg/ProbABEL/examples/mmscore_InvSigma_aj.sex.age.dat
Modified:
pkg/ProbABEL/examples/Makefile.am
Log:
Added some examples to ProbABEL's example directory. The shell scripts are based on their counterparts in the checks directory. Also copied back the genotype data from the checks directory.
Modified: pkg/ProbABEL/examples/Makefile.am
===================================================================
--- pkg/ProbABEL/examples/Makefile.am 2013-08-25 19:43:22 UTC (rev 1313)
+++ pkg/ProbABEL/examples/Makefile.am 2013-08-25 20:13:23 UTC (rev 1314)
@@ -1,3 +1,41 @@
## Process this file with automake to produce Makefile.in
AUTOMAKE_OPTIONS = foreign
+
+phenofiles = height.txt \
+ logist_data.txt \
+ mmscore_pheno.PHE \
+ coxph_data.txt
+
+gtdatadir = gtdata
+genofiles = $(gtdatadir)/test.mldose \
+ $(gtdatadir)/test.mlprob \
+ $(gtdatadir)/test.mlinfo \
+ $(gtdatadir)/test.map \
+ $(gtdatadir)/test.dose.fvi \
+ $(gtdatadir)/test.dose.fvd \
+ $(gtdatadir)/test.prob.fvi \
+ $(gtdatadir)/test.prob.fvd \
+ $(gtdatadir)/mmscore_gen.mlinfo \
+ $(gtdatadir)/mmscore_gen.mldose \
+ $(gtdatadir)/mmscore_gen.mlprob \
+ $(gtdatadir)/mmscore_gen.dose.fvi \
+ $(gtdatadir)/mmscore_gen.dose.fvd \
+ $(gtdatadir)/mmscore_gen.prob.fvi \
+ $(gtdatadir)/mmscore_gen.prob.fvd
+
+
+additional_files = mmscore.R \
+ mmscore_InvSigma_aj.sex.age.dat \
+ README
+
+example_SCRIPTS = example_qt.sh \
+ example_bt.sh \
+ example_cox.sh \
+ example_mmscore.sh
+
+exampledir = $(pkgdatadir)/examples
+dist_example_DATA = $(phenofiles) $(additional_files)
+
+gdatadir = $(pkgdatadir)/examples/gtdata
+dist_gdata_DATA = $(genofiles)
Copied: pkg/ProbABEL/examples/example_bt.sh (from rev 1301, pkg/ProbABEL/checks/test_bt.sh)
===================================================================
--- pkg/ProbABEL/examples/example_bt.sh (rev 0)
+++ pkg/ProbABEL/examples/example_bt.sh 2013-08-25 20:13:23 UTC (rev 1314)
@@ -0,0 +1,54 @@
+#!/bin/bash
+# This script shows some examples on how to run ProbABEL's palogist
+# module for binary traits.
+
+# Set the name of the directory with the genotype data files
+gtdatadir="gtdata"
+
+# Set the path to the executables (palinear/palogist/pacoxph). If you
+# installed ProbABEL according to the instructions in the doc/INSTALL
+# file, or installed it via your Linux distribution's package manager,
+# you can leave this variable empty.
+padir="../src/"
+
+
+# Using text-based dosage genotype files as input
+${padir}palogist \
+ -p logist_data.txt \
+ -d ${inputdir}/test.mldose \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 \
+ -o logist
+
+
+# Using filevector (DatABEL) files as dosage genotype input
+${padir}palogist \
+ -p logist_data.txt \
+ -d ${inputdir}/test.dose.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 \
+ -o logist_fv
+
+
+# Using text-based probability files as genotype input
+${padir}palogist \
+ -p logist_data.txt \
+ -d ${inputdir}/test.mlprob \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ --ngpreds=2 \
+ -c 19 \
+ -o logist_prob
+
+
+# Using filevector (DatABEL) probability files as genotype input
+${padir}palogist \
+ -p logist_data.txt \
+ -d ${inputdir}/test.prob.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ --ngpreds=2 \
+ -c 19 \
+ -o logist_prob_fv
Copied: pkg/ProbABEL/examples/example_cox.sh (from rev 1301, pkg/ProbABEL/checks/test_cox.sh)
===================================================================
--- pkg/ProbABEL/examples/example_cox.sh (rev 0)
+++ pkg/ProbABEL/examples/example_cox.sh 2013-08-25 20:13:23 UTC (rev 1314)
@@ -0,0 +1,53 @@
+#!/bin/bash
+# This script shows some examples for ProbABEL's pacoxph module
+
+# Set the name of the directory with the genotype data files
+gtdatadir="gtdata"
+
+# Set the path to the executables (palinear/palogist/pacoxph). If you
+# installed ProbABEL according to the instructions in the doc/INSTALL
+# file, or installed it via your Linux distribution's package manager,
+# you can leave this variable empty.
+padir="../src/"
+
+
+# Using text-based dosage genotype files as input
+${padir}pacoxph \
+ -p coxph_data.txt \
+ -d ${inputdir}/test.mldose \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 \
+ -o coxph_dose
+
+
+# Using filevector (DatABEL) files as dosage genotype input
+${padir}pacoxph \
+ -p coxph_data.txt \
+ -d ${inputdir}/test.dose.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 \
+ -o coxph_dose_fv
+
+
+# Using text-based probability files as genotype input
+${padir}pacoxph \
+ -p coxph_data.txt \
+ -d ${inputdir}/test.mlprob \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ --ngpreds=2 \
+ -c 19 \
+ -o coxph_prob
+
+
+# Using filevector (DatABEL) probability files as genotype input
+${padir}pacoxph \
+ -p coxph_data.txt \
+ -d ${inputdir}/test.prob.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ --ngpreds=2 \
+ -c 19 \
+ -o coxph_prob_fv
Copied: pkg/ProbABEL/examples/example_mmscore.sh (from rev 1301, pkg/ProbABEL/checks/test_mms.sh)
===================================================================
--- pkg/ProbABEL/examples/example_mmscore.sh (rev 0)
+++ pkg/ProbABEL/examples/example_mmscore.sh 2013-08-25 20:13:23 UTC (rev 1314)
@@ -0,0 +1,54 @@
+#!/bin/bash
+# This script shows some examples on how to run ProbABEL's palinear
+# module for quantitative traits combined with the mmscore option. See
+# also the mmscore.R file on how to prepare the phenotype and
+# inverse-sigma files.
+
+# Set the name of the directory with the genotype data files
+gtdatadir="gtdata"
+
+# Set the path to the executables (palinear/palogist/pacoxph). If you
+# installed ProbABEL according to the instructions in the doc/INSTALL
+# file, or installed it via your Linux distribution's package manager,
+# you can leave this variable empty.
+padir="../src/"
+
+
+# Using text-based dosage genotype files as input
+${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 ${gtdatadir}/mmscore_gen.prob.fvi \
+ --ngpreds=2 --sep="," \
+ -o mmscore_prob_fv \
+ --mmscore mmscore_InvSigma_aj.sex.age.dat
Copied: pkg/ProbABEL/examples/example_qt.sh (from rev 1301, pkg/ProbABEL/checks/test_qt.sh)
===================================================================
--- pkg/ProbABEL/examples/example_qt.sh (rev 0)
+++ pkg/ProbABEL/examples/example_qt.sh 2013-08-25 20:13:23 UTC (rev 1314)
@@ -0,0 +1,134 @@
+#!/bin/bash
+# This script shows some examples on how to run ProbABEL's palinear
+# module for quantitative traits.
+
+
+# Set the name of the directory with the genotype data files
+gtdatadir="gtdata"
+
+# Set the path to the executables (palinear/palogist/pacoxph). If you
+# installed ProbABEL according to the instructions in the doc/INSTALL
+# file, or installed it via your Linux distribution's package manager,
+# you can leave this variable empty.
+padir="${padir}"
+
+# Using text-based dosage genotype files as input
+echo "basic analysis"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.mldose \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 \
+ -o height_base
+
+
+# Using filevector (DatABEL) files as dosage genotype input
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.dose.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 \
+ -o height_base_fv
+
+
+echo "Option --allcov"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.dose.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --allcov \
+ -o height_allcov_fv
+
+
+echo "Option --interaction=1"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.dose.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --interaction=1 \
+ -o height_int1_fv
+
+
+echo "Option --robust"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.dose.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --robust \
+ -o height_robust_fv
+
+
+echo "Option --robust --interaction=1"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.dose.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --robust --interaction=1 \
+ -o height_robust_int1_fv
+
+
+# Using text-based probability files as genotype input
+echo "Option --ngp=2, mlprob file"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.mlprob \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --ngp=2 \
+ -o height_ngp2
+
+
+# Using filevector (DatABEL) probability files as genotype input
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.prob.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --ngp=2 \
+ -o height_ngp2_fv
+
+
+echo "Option --ngp=2 --allcov"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.prob.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --ngp=2 --allcov \
+ -o height_ngp2_allcov_fv
+
+
+echo "Option --ngp=2 --interaction=1"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.prob.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --ngp=2 --interaction=1 \
+ -o height_ngp2_int1_fv
+
+
+echo "Option --ngp=2 --robust"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.prob.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --ngp=2 --robust \
+ -o height_ngp2_robust_fv
+
+
+echo "Option --ngp=2 --robust --interaction=1"
+${padir}palinear \
+ -p height.txt \
+ -d ${inputdir}/test.prob.fvi \
+ -i ${inputdir}/test.mlinfo \
+ -m ${inputdir}/test.map \
+ -c 19 --ngp=2 --robust --interaction=1 \
+ -o height_ngp2_robust_int1_fv
Copied: pkg/ProbABEL/examples/gtdata/mmscore_gen.dose.fvd (from rev 1301, pkg/ProbABEL/checks/inputfiles/mmscore_gen.dose.fvd)
===================================================================
(Binary files differ)
Copied: pkg/ProbABEL/examples/gtdata/mmscore_gen.dose.fvi (from rev 1301, pkg/ProbABEL/checks/inputfiles/mmscore_gen.dose.fvi)
===================================================================
(Binary files differ)
Copied: pkg/ProbABEL/examples/gtdata/mmscore_gen.mldose (from rev 1301, pkg/ProbABEL/checks/inputfiles/mmscore_gen.mldose)
===================================================================
--- pkg/ProbABEL/examples/gtdata/mmscore_gen.mldose (rev 0)
+++ pkg/ProbABEL/examples/gtdata/mmscore_gen.mldose 2013-08-25 20:13:23 UTC (rev 1314)
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Copied: pkg/ProbABEL/examples/gtdata/mmscore_gen.mlinfo (from rev 1301, pkg/ProbABEL/checks/inputfiles/mmscore_gen.mlinfo)
===================================================================
--- pkg/ProbABEL/examples/gtdata/mmscore_gen.mlinfo (rev 0)
+++ pkg/ProbABEL/examples/gtdata/mmscore_gen.mlinfo 2013-08-25 20:13:23 UTC (rev 1314)
@@ -0,0 +1,6 @@
+SNP Al1 Al2 Freq1 MAF Quality Rsq
+rs735579 A B 0.5847 0.5847 0.5847 0.5847
+rs9088604 A B 0.5847 0.5847 0.5847 0.5847
+rs1413801 A B 0.5847 0.5847 0.5847 0.5847
+rs4911638 A B 0.5847 0.5847 0.5847 0.5847
+rs70099 A B 0.5847 0.5847 0.5847 0.5847
Copied: pkg/ProbABEL/examples/gtdata/mmscore_gen.mlprob (from rev 1301, pkg/ProbABEL/checks/inputfiles/mmscore_gen.mlprob)
===================================================================
--- pkg/ProbABEL/examples/gtdata/mmscore_gen.mlprob (rev 0)
+++ pkg/ProbABEL/examples/gtdata/mmscore_gen.mlprob 2013-08-25 20:13:23 UTC (rev 1314)
@@ -0,0 +1,500 @@
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+1->id3330 MLPROB 0 0 0 1 0 0 0 1 0 0
+1->id3354 MLPROB NaN NaN 0 1 0 0 0 0 NaN NaN
+1->id3371 MLPROB 0 1 0 1 0 1 0 0 0 0
+1->id3398 MLPROB 0 1 0 1 1 0 0 1 NaN NaN
+1->id3400 MLPROB 0 1 1 0 0 0 0 1 0 0
+1->id3417 MLPROB 0 1 0 1 0 0 0 1 0 0
+1->id3465 MLPROB 0 1 0 1 0 0 0 1 0 0
+1->id3521 MLPROB 1 0 0 0 0 0 0 0 0 0
+1->id3573 MLPROB 0 1 0 1 0 1 0 0 0 0
+1->id3593 MLPROB 1 0 0 1 0 1 0 0 0 0
+1->id3630 MLPROB 1 0 1 0 0 0 0 0 0 0
+1->id3635 MLPROB 0 1 0 1 0 0 0 1 0 0
+1->id3641 MLPROB 1 0 0 0 0 0 0 1 0 0
+1->id3657 MLPROB 0 1 0 1 1 0 0 0 0 1
+1->id3692 MLPROB 1 0 0 1 0 0 0 0 0 0
+1->id3701 MLPROB 0 1 1 0 1 0 0 1 0 1
+1->id3709 MLPROB 1 0 0 1 0 0 0 0 0 0
+1->id3735 MLPROB 0 1 0 1 0 1 0 0 0 0
+1->id3809 MLPROB 0 0 0 1 1 0 0 0 0 0
+1->id3820 MLPROB 1 0 0 0 0 1 0 0 0 0
+1->id3823 MLPROB 0 0 0 1 1 0 0 1 1 0
+1->id3828 MLPROB 0 0 0 0 0 0 0 0 0 0
+1->id3831 MLPROB 0 0 0 1 0 1 0 0 0 1
+1->id3847 MLPROB 0 1 0 0 0 0 0 0 0 0
+1->id3857 MLPROB 0 1 1 0 0 0 0 1 0 0
+1->id3933 MLPROB 0 0 1 0 0 0 0 0 0 0
+1->id3934 MLPROB 0 1 0 1 0 1 0 0 0 1
+1->id3942 MLPROB 1 0 0 1 0 1 0 0 0 0
+1->id3957 MLPROB 0 1 0 1 0 1 0 0 0 1
+1->id3970 MLPROB 0 0 0 1 1 0 0 0 1 0
+1->id3983 MLPROB 0 1 0 1 0 0 0 1 0 0
+1->id4008 MLPROB 0 0 0 1 0 1 0 1 0 0
+1->id4024 MLPROB 0 1 0 1 0 1 0 0 0 0
+1->id4031 MLPROB 0 1 0 0 1 0 0 0 0 1
+1->id4067 MLPROB 1 0 0 1 0 1 0 0 0 0
+1->id4097 MLPROB 0 1 1 0 0 1 0 1 0 0
+1->id4225 MLPROB 1 0 1 0 0 0 0 0 0 0
+1->id4229 MLPROB 1 0 0 1 0 0 0 0 0 0
+1->id4233 MLPROB 0 0 0 1 0 0 0 0 0 0
+1->id4254 MLPROB 0 1 0 1 0 0 0 0 0 0
+1->id4259 MLPROB 0 1 0 0 0 0 0 0 0 0
+1->id4261 MLPROB 1 0 0 1 0 1 0 0 0 0
+1->id4284 MLPROB 0 1 0 0 1 0 0 1 0 0
+1->id4287 MLPROB 0 1 0 1 0 1 0 0 0 1
+1->id4288 MLPROB 0 0 0 0 0 1 0 0 0 1
+1->id4309 MLPROB 1 0 0 1 0 1 0 0 0 0
+1->id4328 MLPROB 0 0 1 0 0 0 0 1 0 0
+1->id4337 MLPROB 0 1 0 0 0 1 0 0 0 0
+1->id4363 MLPROB 0 0 0 1 1 0 0 1 0 1
+1->id4380 MLPROB 0 0 0 1 0 1 0 0 0 1
+1->id4395 MLPROB 0 0 0 1 0 0 0 0 0 0
+1->id4416 MLPROB 0 0 1 0 0 1 0 0 0 0
+1->id4446 MLPROB 0 1 0 1 0 0 0 0 0 0
+1->id4449 MLPROB 0 1 1 0 0 1 0 0 0 1
+1->id4512 MLPROB 0 1 0 1 0 1 0 0 0 0
+1->id4552 MLPROB 0 1 0 1 0 1 0 1 0 0
+1->id4561 MLPROB 1 0 0 1 0 0 0 0 0 0
+1->id4606 MLPROB 0 1 0 1 0 1 0 1 0 1
+1->id4629 MLPROB 1 0 0 1 0 1 0 0 0 0
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1314
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