diff options
Diffstat (limited to 'sourcecodes/data/example2')
21 files changed, 1154 insertions, 0 deletions
diff --git a/sourcecodes/data/example2/hQGban.txt b/sourcecodes/data/example2/hQGban.txt new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example2/hQGban.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/example2/hQGcontinuous_input.txt b/sourcecodes/data/example2/hQGcontinuous_input.txt new file mode 100644 index 00000000..5e296c45 --- /dev/null +++ b/sourcecodes/data/example2/hQGcontinuous_input.txt @@ -0,0 +1,203 @@ +Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 +2 2 1 1 1 1 1 1 +2 2 0.46259 1.2692 -1.3164 -0.44096 0.5929 -0.75422 +1 1 -0.10011 -0.88834 1.6407 0.99972 0.31288 0.65602 +1 1 -1.0533 -0.55296 1.2715 1.3686 -0.19153 0.37361 +1 2 0.042371 0.13573 -0.72659 -0.66133 0.43157 -1.6715 +1 2 -0.68686 -1.6152 -0.95019 -1.2239 0.12319 -0.79155 +1 1 -0.4558 0.090877 0.94224 1.2354 -0.36356 0.34937 +1 1 0.237 -0.49002 1.8939 1.4399 0.033059 1.3229 +1 2 0.070265 0.22547 -1.4903 -0.069341 -0.16148 -0.01449 +1 1 -0.69146 -0.43461 1.1501 0.21205 -0.18087 0.32746 +1 1 0.31535 -0.9858 0.57816 0.35924 0.12866 1.0553 +2 1 1.2718 0.39314 0.6669 0.90002 -0.30206 1.3376 +1 1 1.1871 -0.45611 0.87227 0.31014 -0.092846 0.81278 +2 1 -1.0168 -0.44286 1.6933 0.72968 0.038808 0.81906 +2 2 -0.25313 0.52468 0.02823 -0.20984 -0.075809 -1.3591 +1 2 -0.58108 -0.3967 -0.11925 -0.61288 0.46778 0.090941 +1 2 -0.88043 -0.28187 -1.1645 -1.2543 -0.28951 -1.039 +1 2 0.54121 0.24395 -1.0043 -1.4483 -0.19839 -2.5407 +2 1 0.47375 1.1319 0.68553 1.035 0.44043 1.3011 +2 1 0.57785 0.69093 1.5941 1.6735 0.19981 0.50708 +1 2 -0.43989 0.0024131 -1.5405 -1.2304 -0.15382 -1.1058 +2 1 0.38035 -0.063535 1.1606 1.3124 -0.38043 0.6277 +1 2 0.70114 -0.41044 -0.39767 -1.5424 0.27477 -0.76183 +1 1 -0.9406 -0.20526 1.3302 1.097 0.16006 1.2988 +1 2 0.52122 0.064793 -0.031492 0.21696 -0.41979 -0.79123 +1 2 -0.53387 -0.71043 -0.52344 -1.5584 -0.09538 -1.5781 +1 1 0.49563 -0.58126 0.7747 1.274 0.19196 0.10624 +2 2 1.1499 1.879 0.43595 0.73474 0.045381 -0.88645 +1 2 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a/sourcecodes/data/example2/hQGk.txt b/sourcecodes/data/example2/hQGk.txt new file mode 100644 index 00000000..29d6383b --- /dev/null +++ b/sourcecodes/data/example2/hQGk.txt @@ -0,0 +1 @@ +100 diff --git a/sourcecodes/data/example2/hQGmap.txt b/sourcecodes/data/example2/hQGmap.txt new file mode 100644 index 00000000..032b8928 --- /dev/null +++ b/sourcecodes/data/example2/hQGmap.txt @@ -0,0 +1,8 @@ +Geno1 1 0.473175 1.335000 +Geno2 2 0.496318 1.570000 +Trait1 1 0.668009 -0.023903 +Trait2 1 0.796873 0.038552 +Trait3 2 1.036694 0.068708 +Trait4 1 0.984008 -0.010125 +Trait5 1 0.316471 0.008911 +Trait6 1 0.904542 -0.114267 diff --git a/sourcecodes/data/example2/hQGmapdata.txt b/sourcecodes/data/example2/hQGmapdata.txt new file mode 100644 index 00000000..42b2fd9c --- /dev/null +++ b/sourcecodes/data/example2/hQGmapdata.txt @@ -0,0 +1 @@ +Trait5 Geno2 Trait6 Trait3 Geno1 Trait2 Trait4 Trait1 diff --git a/sourcecodes/data/example2/hQGname.txt b/sourcecodes/data/example2/hQGname.txt new file mode 100644 index 00000000..8f42b468 --- /dev/null +++ b/sourcecodes/data/example2/hQGname.txt @@ -0,0 +1 @@ +Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 diff --git a/sourcecodes/data/example2/hQGnet_figure.txt b/sourcecodes/data/example2/hQGnet_figure.txt new file mode 100644 index 00000000..893f9f14 --- /dev/null +++ b/sourcecodes/data/example2/hQGnet_figure.txt @@ -0,0 +1,652 @@ +8 +1200 1200 +Trait5 0 0 +Geno2 300 0 +Trait6 120 300 +Trait3 420 300 +Geno1 600 0 +Trait2 720 300 +Trait4 100 600 +Trait1 500 600 +Trait5 1 +250 150 +0 +0 +-3.2055 0.0025 +-3.1368 0.0030 +-3.0681 0.0038 +-2.9994 0.0046 +-2.9308 0.0057 +-2.8621 0.0069 +-2.7934 0.0083 +-2.7247 0.0101 +-2.6561 0.0121 +-2.5874 0.0144 +-2.5187 0.0172 +-2.4500 0.0203 +-2.3813 0.0240 +-2.3127 0.0281 +-2.2440 0.0328 +-2.1753 0.0381 +-2.1066 0.0441 +-2.0379 0.0508 +-1.9693 0.0582 +-1.9006 0.0664 +-1.8319 0.0754 +-1.7632 0.0852 +-1.6945 0.0958 +-1.6259 0.1073 +-1.5572 0.1195 +-1.4885 0.1326 +-1.4198 0.1463 +-1.3511 0.1608 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0.0028 +3.2416 0.0022 +3.3195 0.0017 +3.3973 0.0013 +3.4752 0.0010 +3.5530 0.0008 +3.6309 0.0006 +3.7087 0.0004 +3.7866 0.0003 +3.8645 0.0002 +3.9423 0.0002 +4.0202 0.0001 +4.0980 0.0001 diff --git a/sourcecodes/data/example2/hQGnlevels.txt b/sourcecodes/data/example2/hQGnlevels.txt new file mode 100644 index 00000000..32457058 --- /dev/null +++ b/sourcecodes/data/example2/hQGnlevels.txt @@ -0,0 +1,4 @@ +Geno1 1 2 +Geno2 1 2 + + diff --git a/sourcecodes/data/example2/hQGnnode.txt b/sourcecodes/data/example2/hQGnnode.txt new file mode 100644 index 00000000..45a4fb75 --- /dev/null +++ b/sourcecodes/data/example2/hQGnnode.txt @@ -0,0 +1 @@ +8 diff --git a/sourcecodes/data/example2/hQGnrows.txt b/sourcecodes/data/example2/hQGnrows.txt new file mode 100644 index 00000000..3bc92d44 --- /dev/null +++ b/sourcecodes/data/example2/hQGnrows.txt @@ -0,0 +1 @@ +201 diff --git a/sourcecodes/data/example2/hQGparent.txt b/sourcecodes/data/example2/hQGparent.txt new file mode 100644 index 00000000..b8626c4c --- /dev/null +++ b/sourcecodes/data/example2/hQGparent.txt @@ -0,0 +1 @@ +4 diff --git a/sourcecodes/data/example2/hQGrun_initialstructure.sh b/sourcecodes/data/example2/hQGrun_initialstructure.sh new file mode 100644 index 00000000..7d4cbfea --- /dev/null +++ b/sourcecodes/data/example2/hQGrun_initialstructure.sh @@ -0,0 +1,38 @@ +#!/bin/sh +# script for execution of deployed applications +# +# Sets up the MCR environment for the current $ARCH and executes +# the specified command. +# +exe_name=$0 +exe_dir=`dirname "$0"` +echo "------------------------------------------" +if [ "x$1" = "x" ]; then + echo Usage: + echo $0 \<deployedMCRroot\> args +else + echo Setting up environment variables + MCRROOT="$1" + echo --- + LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ; + LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ; + LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64; + MCRJRE=${MCRROOT}/sys/java/jre/glnxa64/jre/lib/amd64 ; + LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/native_threads ; + LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/server ; + LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE}/client ; + LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRJRE} ; + XAPPLRESDIR=${MCRROOT}/X11/app-defaults ; + export LD_LIBRARY_PATH; + export XAPPLRESDIR; + echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH}; + shift 1 + args= + while [ $# -gt 0 ]; do + token=`echo "$1" | sed 's/ /\\\\ /g'` # Add blackslash before each blank + args="${args} ${token}" + shift + done + "${exe_dir}"/initialstructure hQG +fi +exit diff --git a/sourcecodes/data/example2/hQGstructure_input.txt b/sourcecodes/data/example2/hQGstructure_input.txt new file mode 100644 index 00000000..410c0fa4 --- /dev/null +++ b/sourcecodes/data/example2/hQGstructure_input.txt @@ -0,0 +1,9 @@ +Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 +0 0 0 1 0 0 0 0 +0 0 0 0 1 1 0 1 +0 0 0 0 0 0 0 0 +0 0 1 0 0 1 0 0 +0 0 0 0 0 1 0 0 +0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 diff --git a/sourcecodes/data/example2/hQGstructure_input_temp.txt b/sourcecodes/data/example2/hQGstructure_input_temp.txt new file mode 100644 index 00000000..63380a62 --- /dev/null +++ b/sourcecodes/data/example2/hQGstructure_input_temp.txt @@ -0,0 +1,9 @@ +Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 +0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.350069 0.000000 +0.030654 0.000000 0.049399 0.000000 1.000000 1.000000 0.000000 1.000000 +0.000000 0.000000 0.000000 0.000000 0.025163 0.000000 0.123845 0.000000 +0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.053585 0.000000 +0.000000 0.000000 0.000000 0.108604 0.000000 1.000000 0.010570 0.000000 +0.000000 0.000000 0.013713 0.000000 0.000000 0.000000 0.011282 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.137567 +0.000000 0.000000 0.136004 0.056792 0.457123 0.029978 0.000000 0.000000 diff --git a/sourcecodes/data/example2/hQGstructure_old.txt b/sourcecodes/data/example2/hQGstructure_old.txt new file mode 100644 index 00000000..f979ea93 --- /dev/null +++ b/sourcecodes/data/example2/hQGstructure_old.txt @@ -0,0 +1,7 @@ +Geno1 0.6650 0.3350 +Trait2 0.0037 0.0045 0.0055 0.0067 0.0081 0.0097 0.0116 0.0139 0.0165 0.0195 0.0229 0.0268 0.0313 0.0363 0.0420 0.0483 0.0553 0.0631 0.0716 0.0809 0.0910 0.1019 0.1135 0.1260 0.1392 0.1530 0.1675 0.1826 0.1981 0.2139 0.2300 0.2462 0.2623 0.2782 0.2937 0.3088 0.3231 0.3366 0.3490 0.3603 0.3703 0.3788 0.3858 0.3912 0.3948 0.3967 0.3968 0.3951 0.3916 0.3865 0.3796 0.3713 0.3614 0.3503 0.3379 0.3246 0.3103 0.2954 0.2799 0.2640 0.2479 0.2317 0.2156 0.1998 0.1842 0.1691 0.1546 0.1406 0.1274 0.1148 0.1031 0.0921 0.0819 0.0725 0.0640 0.0561 0.0490 0.0426 0.0369 0.0318 0.0273 0.0233 0.0198 0.0168 0.0141 0.0119 0.0099 0.0082 0.0068 0.0056 0.0046 0.0038 0.0031 0.0025 0.0020 0.0016 0.0013 0.0010 0.0008 0.0006 0.0005 +Geno2 0.4300 0.5700 +Trait3 0.0086 0.0101 0.0119 0.0140 0.0163 0.0190 0.0220 0.0254 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-0,0 +1 @@ +0.5 diff --git a/sourcecodes/data/example2/hQGtier.txt b/sourcecodes/data/example2/hQGtier.txt new file mode 100644 index 00000000..bc94239b --- /dev/null +++ b/sourcecodes/data/example2/hQGtier.txt @@ -0,0 +1 @@ +3,Tier1,0,Tier2,0,Tier3,0, \ No newline at end of file diff --git a/sourcecodes/data/example2/hQGtype.txt b/sourcecodes/data/example2/hQGtype.txt new file mode 100644 index 00000000..285a68af --- /dev/null +++ b/sourcecodes/data/example2/hQGtype.txt @@ -0,0 +1,2 @@ +Geno1 Geno2 Trait1 Trait2 Trait3 Trait4 Trait5 Trait6 +2 2 1 1 1 1 1 1 diff --git a/sourcecodes/data/example2/hQGwhite.txt b/sourcecodes/data/example2/hQGwhite.txt new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example2/hQGwhite.txt @@ -0,0 +1 @@ +From To diff --git a/sourcecodes/data/example2/standardized_data.txt b/sourcecodes/data/example2/standardized_data.txt new file mode 100644 index 00000000..743e8b02 --- /dev/null +++ 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