diff options
Diffstat (limited to 'sourcecodes/data/example_chr2_spleen')
22 files changed, 2981 insertions, 0 deletions
diff --git a/sourcecodes/data/example_chr2_spleen/cuLban.txt b/sourcecodes/data/example_chr2_spleen/cuLban.txt new file mode 100644 index 00000000..fdd12dda --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLban.txt @@ -0,0 +1,51 @@ +From To +Ifih1 rs3664317 +Oas1a rs3664317 +Parp9 rs3664317 +Dhx58 rs3664317 +Cd1d1 rs3664317 +Irf7 rs3664317 +Oas3 rs3664317 +Pml rs3664317 +Mx1 rs3664317 +Ifit1 rs3664317 +Trim25 rs3664317 +Oas1g rs3664317 +Pglyrp3 rs3664317 +Ifih1 rs3664317 +Oas1a Ifih1 +Parp9 Ifih1 +Dhx58 Ifih1 +Cd1d1 Ifih1 +Irf7 Ifih1 +Oas3 Ifih1 +Pml Ifih1 +Mx1 Ifih1 +Ifit1 Ifih1 +Trim25 Ifih1 +Oas1g Ifih1 +Pglyrp3 Ifih1 +Oas1a rs3664317 +Parp9 rs3664317 +Dhx58 rs3664317 +Cd1d1 rs3664317 +Irf7 rs3664317 +Oas3 rs3664317 +Pml rs3664317 +Mx1 rs3664317 +Ifit1 rs3664317 +Trim25 rs3664317 +Oas1g rs3664317 +Pglyrp3 rs3664317 +Oas1a Ifih1 +Parp9 Ifih1 +Dhx58 Ifih1 +Cd1d1 Ifih1 +Irf7 Ifih1 +Oas3 Ifih1 +Pml Ifih1 +Mx1 Ifih1 +Ifit1 Ifih1 +Trim25 Ifih1 +Oas1g Ifih1 +Pglyrp3 Ifih1 diff --git a/sourcecodes/data/example_chr2_spleen/cuLcontinuous_input.txt b/sourcecodes/data/example_chr2_spleen/cuLcontinuous_input.txt new file mode 100644 index 00000000..ca8ea1e5 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLcontinuous_input.txt @@ -0,0 +1,76 @@ +rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 +2 1 1 1 1 1 1 1 1 1 1 1 1 1 +1 8.34 9.812 8.774 9.79 9.663 8.27 11.036 7.284 8.286 10.395 8.521 6.186 8.83 +1 8.368 9.738 8.566 9.144 9.484 8.818 11.03 6.977 8.294 10.076 8.529 5.968 8.828 +1 8.178 9.57 8.726 9.575 10.106 8.99 10.878 7.205 8.676 10.036 8.61 5.976 9.024 +1 8.116 9.901 8.904 9.959 9.793 8.336 11.105 7.598 8.316 10.292 8.401 5.814 8.836 +2 8.099 9.68 8.876 10.116 9.771 8.379 11.028 7.438 8.541 10.215 8.32 5.917 9.073 +1 8.262 9.59 8.24 10.088 8.938 7.832 10.486 6.752 7.825 9.908 8.196 6.15 8.446 +1 7.915 9.415 8.308 9.707 9.12 8.702 11.102 7.208 8.243 10.034 7.897 6.06 8.892 +2 8.565 10.002 8.96 9.779 10.322 9.24 11.278 7.644 8.893 10.42 8.773 5.914 9.407 +1 8.189 9.774 8.541 9.939 9.134 7.819 10.766 7.122 8.352 10.113 8.492 6.269 9.055 +1 8.476 9.954 8.908 9.476 9.92 8.764 11.134 7.859 8.788 10.17 8.862 6.226 9.17 +2 8.119 9.946 8.876 9.578 10.02 8.734 11.244 7.85 8.838 10.557 8.56 5.98 9.353 +2 8.305 9.713 8.972 9.789 9.839 8.804 10.948 7.682 8.896 10.181 8.854 5.979 9.567 +2 8.654 10 9.306 9.439 10.457 9.223 10.922 7.082 8.942 10.131 9.162 6.01 9.74 +1 8.105 9.748 8.725 10.119 9.782 8.575 11.113 7.63 8.674 10.355 8.59 6.279 8.908 +1 8.247 9.715 8.829 9.646 9.953 9.668 11.112 7.384 9.221 10.19 8.64 6 9.552 +1 8.511 9.994 9.014 9.89 10.266 8.444 10.599 7.331 9.153 10.012 8.837 6.148 9.023 +2 8.947 10.28 9.483 9.398 11.23 9.86 11.324 8.006 9.772 10.524 9.587 5.865 10.067 +1 8.526 9.685 8.921 9.7 10.126 9.373 11.121 7.497 9.003 10.357 8.156 6.334 9.678 +2 8.06 9.745 9.092 9.278 10.231 8.976 10.998 7.578 9.145 10.283 8.611 6.168 9.413 +2 7.93 9.728 8.694 9.512 9.826 9.016 11.276 7.604 8.767 10.378 8.577 5.963 9.264 +2 8.511 9.686 9.014 8.982 10.508 10.108 11.304 7.441 9.133 10.341 9.04 6.2 9.974 +2 8.645 9.997 8.97 9.443 10.393 9.302 11.409 7.785 8.894 10.552 9.051 5.997 9.412 +2 8.293 9.802 9.001 9.524 10.156 9.263 11.212 7.772 8.581 10.433 8.514 6.093 9.177 +1 7.781 9.712 8.97 9.375 10.12 9.484 11.317 7.347 8.972 10.393 8.352 6.193 9.587 +2 8.465 9.88 8.913 9.816 9.965 8.852 11.138 7.537 8.625 10.426 8.617 6.044 9.556 +2 8.657 10.026 9.189 9.691 10.302 9.268 11.194 7.634 9.143 10.378 9.05 6.067 9.679 +2 7.634 9.606 8.36 9.465 8.41 8.605 11.183 6.942 8.174 9.952 7.478 6.09 9.535 +1 7.669 9.494 8.779 9.552 9.362 8.52 11.024 7.131 8.378 10.391 8.114 6.07 8.851 +2 8.618 10.212 9.433 9.672 10.442 9.21 11.328 8.045 9.322 10.5 9.128 5.994 9.656 +2 8.731 10.27 9.342 9.43 10.697 10.117 11.286 7.749 9.734 10.464 9.322 6.156 9.876 +1 7.554 9.524 8.759 9.93 9.52 8.279 10.82 7.32 8.316 10.31 8.186 6.068 9.046 +1 8.262 9.677 8.75 9.444 10.052 8.634 10.888 7.32 8.562 9.893 8.644 6.212 8.918 +1 7.823 9.628 8.66 9.529 9.578 8.736 11.206 7.171 8.408 10.062 8.111 5.838 9.033 +1 8.28 9.572 8.784 9.428 9.862 9.424 11.27 7.288 8.505 10.174 8.642 6.022 9.313 +2 9.09 10.053 9.599 9.469 11.004 9.882 11.436 8.521 9.814 10.562 9.704 6.044 10.061 +1 8.446 9.989 9.297 9.688 10.577 9.129 11.102 7.718 9.484 10.231 9.072 6.17 9.21 +1 8.668 9.858 9.195 9.385 10.695 9.249 11.028 7.765 9.367 10.319 9.179 6.136 9.563 +2 8.574 10.059 9.281 9.233 10.508 9.247 11.145 8.138 9.505 10.402 9.192 5.992 9.848 +2 8.523 10.052 9.131 9.507 10.418 9.413 11.187 7.641 9.304 10.465 9.063 6.095 9.733 +1 7.987 9.748 8.766 9.578 9.781 8.482 11.279 7.52 8.364 10.141 8.207 6.192 9.133 +2 8.466 9.429 8.946 9.395 9.715 9.071 11.388 7.592 8.078 10.32 8.326 6.108 9.021 +1 7.668 9.694 8.493 10.112 9.561 8.394 10.922 7.26 8.19 10.27 7.916 5.892 8.974 +2 8.379 10.037 9.155 9.683 10.281 9.2 10.913 7.173 9.404 10.381 9.097 6.099 9.714 +2 7.805 9.654 8.454 9.198 10.065 9.468 11.217 6.917 8.43 10.459 8.11 6.068 9.068 +1 7.981 9.8 8.553 9.946 9.862 8.901 11.085 7.214 8.393 10.373 8.19 6.05 9.015 +1 7.746 9.688 8.578 9.901 9.358 7.866 10.928 7.354 7.929 10.233 8.066 5.754 8.883 +1 7.997 9.859 8.795 9.867 9.817 8.734 11.109 7.416 8.67 10.247 8.176 6.143 9.081 +1 8.674 9.689 9.06 9.81 10.544 8.995 11.189 7.781 9.219 10.07 8.98 5.992 9.143 +1 8.088 9.49 8.676 9.456 10.184 8.737 10.998 7.222 8.538 10.192 8.441 6.147 8.55 +1 8.001 9.801 8.669 9.977 9.383 8.274 11.055 7.231 7.913 10.272 8.277 5.931 9.009 +2 8.218 9.458 8.781 9.214 9.66 8.87 10.738 7.241 8.289 10.029 8.612 6.125 9.38 +1 7.684 9.56 8.75 10.077 9.686 8.27 11.102 7.206 8.13 10.212 8.07 6.018 8.984 +2 8.326 9.696 8.88 9.714 10.014 9.08 11.055 7.256 8.494 10.054 8.63 6.177 9.162 +2 8.906 10.106 9.412 9.704 11.06 9.854 11.335 7.799 10.103 10.471 9.25 6.033 9.97 +1 8.073 9.793 8.626 9.879 9.262 8.408 10.844 7.108 8.368 9.959 8.261 6.052 8.916 +2 8.527 10.026 9.143 9.244 10.597 9.566 11.108 7.778 9.748 10.351 9.153 6.055 9.698 +2 8.614 10.05 9.202 9.508 10.66 9.63 11.156 7.758 9.789 10.324 9.068 6.15 9.948 +2 8.522 10.158 8.992 9.684 9.992 8.55 11.125 7.914 8.976 10.311 8.574 5.889 9.566 +1 8.086 9.6 8.522 9.544 9.641 8.514 10.99 7.386 8.506 10.194 8.234 6.02 8.736 +1 7.873 9.596 8.452 9.422 9.278 8.509 10.958 7.057 8.081 9.981 7.969 6.136 8.958 +2 8.371 9.99 8.949 9.931 10.195 8.935 10.83 7.694 9.183 10.493 9.124 6.128 9.396 +2 8.476 9.982 9.115 9.639 10.465 9.833 11.105 8.058 9.9 10.351 9.182 6.05 9.884 +1 8.512 9.995 8.846 9.951 9.561 8.558 10.769 7.584 8.901 10.139 8.769 5.959 9.203 +1 8.358 9.858 8.99 9.981 10.123 9.368 10.989 7.463 9.327 9.93 8.54 6.02 9.543 +1 8.23 9.614 8.806 9.919 9.939 9.108 11.184 7.766 8.793 10.174 8.605 5.972 9.068 +2 8.238 9.802 8.926 9.595 10.062 8.77 11.202 7.712 9.131 10.34 8.57 6.05 9.464 +1 8.533 10.108 9.083 10.214 10.514 8.463 11.008 7.356 9.344 10.196 8.736 6.262 9.257 +1 7.866 9.444 8.223 9.865 8.95 8.539 10.935 6.754 7.748 10.177 7.826 6.29 8.716 +2 8.888 10.031 9.158 9.407 10.8 9.547 11.238 7.659 9.602 10.398 9.337 6.028 9.529 +1 8.026 9.682 8.398 9.824 9.202 8.041 10.703 7.322 8.352 10.209 8.196 6.009 9.001 +2 8.974 10.071 9.451 9.348 11.061 9.686 11.255 8.077 10.101 10.323 9.557 6.006 10.072 +1 8.181 9.432 9.045 9.544 10.651 9.18 10.832 7.419 8.742 9.818 8.546 6.33 9.201 +1 8.137 9.676 9.024 9.37 10.206 9.944 10.985 7.226 8.9 10.362 8.918 6.352 9.367 + diff --git a/sourcecodes/data/example_chr2_spleen/cuLgraphviz.txt b/sourcecodes/data/example_chr2_spleen/cuLgraphviz.txt new file mode 100644 index 00000000..824e26d5 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLgraphviz.txt @@ -0,0 +1,32 @@ +digraph G { +size="10,10"; ratio = fill; +node [shape=square,width=1.5]; +rs3664317 -> Dhx58; +rs3664317 -> Cd1d1; +rs3664317 -> Ifit1; +rs3664317 -> Oas1g; +rs3664317 -> Ifih1; +Parp9 -> Oas1a; +Dhx58 -> Irf7; +Dhx58 -> Mx1; +Dhx58 -> Ifit1; +Dhx58 -> Trim25; +Dhx58 -> Oas1g; +Cd1d1 -> Oas3; +Cd1d1 -> Trim25; +Cd1d1 -> Pglyrp3; +Oas3 -> Pglyrp3; +Pml -> Oas3; +Pml -> Pglyrp3; +Ifit1 -> Irf7; +Ifit1 -> Mx1; +Trim25 -> Parp9; +Trim25 -> Pml; +Trim25 -> Pglyrp3; +Ifih1 -> Parp9; +Ifih1 -> Dhx58; +Ifih1 -> Cd1d1; +Ifih1 -> Oas3; +Ifih1 -> Ifit1; +Ifih1 -> Trim25; +} \ No newline at end of file diff --git a/sourcecodes/data/example_chr2_spleen/cuLk.txt b/sourcecodes/data/example_chr2_spleen/cuLk.txt new file mode 100644 index 00000000..29d6383b --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLk.txt @@ -0,0 +1 @@ +100 diff --git a/sourcecodes/data/example_chr2_spleen/cuLmap.txt b/sourcecodes/data/example_chr2_spleen/cuLmap.txt new file mode 100644 index 00000000..325f9a8d --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLmap.txt @@ -0,0 +1,14 @@ +rs3664317 2 0.501140 1.452055 +Oas1a 1 0.347301 8.281466 +Parp9 1 0.216211 9.804164 +Dhx58 1 0.302026 8.891247 +Cd1d1 1 0.268738 9.643644 +Irf7 1 0.548579 10.009315 +Oas3 1 0.548788 8.957397 +Pml 1 0.190985 11.075425 +Mx1 1 0.336795 7.483137 +Ifit1 1 0.569192 8.828521 +Trim25 1 0.176657 10.255192 +Oas1g 1 0.458134 8.632151 +Pglyrp3 1 0.123345 6.070877 +Ifih1 1 0.387383 9.298137 diff --git a/sourcecodes/data/example_chr2_spleen/cuLmapdata.txt b/sourcecodes/data/example_chr2_spleen/cuLmapdata.txt new file mode 100644 index 00000000..64d3fc62 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLmapdata.txt @@ -0,0 +1 @@ +rs3664317 Ifih1 Cd1d1 Dhx58 Oas1g Trim25 Pml Oas3 Pglyrp3 Parp9 Oas1a Ifit1 Mx1 Irf7 diff --git a/sourcecodes/data/example_chr2_spleen/cuLname.txt b/sourcecodes/data/example_chr2_spleen/cuLname.txt new file mode 100644 index 00000000..1cc6fe19 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLname.txt @@ -0,0 +1 @@ +rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 diff --git a/sourcecodes/data/example_chr2_spleen/cuLnet_figure.txt b/sourcecodes/data/example_chr2_spleen/cuLnet_figure.txt new file mode 100644 index 00000000..79f052a0 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLnet_figure.txt @@ -0,0 +1,1387 @@ +14 +1200 1400 +rs3664317 360 0 +Ifih1 480 175 +Cd1d1 160 350 +Dhx58 560 350 +Oas1g 180 525 +Trim25 480 525 +Pml 0 700 +Oas3 280 875 +Pglyrp3 360 1050 +Parp9 240 700 +Oas1a 680 875 +Ifit1 780 525 +Mx1 480 700 +Irf7 720 700 +rs3664317 2 +250 150 +0 +5 2 3 4 5 12 +1 0.5479 +2 0.4521 +Ifih1 1 +250 150 +1 1 +6 3 4 6 8 10 12 +-3.1997 0.0023 +-3.1378 0.0028 +-3.0758 0.0034 +-3.0138 0.0041 +-2.9518 0.0050 +-2.8899 0.0060 +-2.8279 0.0071 +-2.7659 0.0085 +-2.7039 0.0101 +-2.6420 0.0119 +-2.5800 0.0140 +-2.5180 0.0164 +-2.4560 0.0192 +-2.3941 0.0223 +-2.3321 0.0259 +-2.2701 0.0299 +-2.2081 0.0343 +-2.1462 0.0393 +-2.0842 0.0449 +-2.0222 0.0510 +-1.9602 0.0578 +-1.8983 0.0652 +-1.8363 0.0733 +-1.7743 0.0820 +-1.7124 0.0914 +-1.6504 0.1015 +-1.5884 0.1124 +-1.5264 0.1238 +-1.4645 0.1359 +-1.4025 0.1487 +-1.3405 0.1620 +-1.2785 0.1758 +-1.2166 0.1900 +-1.1546 0.2046 +-1.0926 0.2195 +-1.0306 0.2345 +-0.9687 0.2496 +-0.9067 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0.0000 +3.0824 0.0000 +3.1538 0.0000 +3.2252 0.0000 diff --git a/sourcecodes/data/example_chr2_spleen/cuLnlevels.txt b/sourcecodes/data/example_chr2_spleen/cuLnlevels.txt new file mode 100644 index 00000000..605579c3 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLnlevels.txt @@ -0,0 +1,2 @@ +rs3664317 1 2 + diff --git a/sourcecodes/data/example_chr2_spleen/cuLnnode.txt b/sourcecodes/data/example_chr2_spleen/cuLnnode.txt new file mode 100644 index 00000000..8351c193 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLnnode.txt @@ -0,0 +1 @@ +14 diff --git a/sourcecodes/data/example_chr2_spleen/cuLnrows.txt b/sourcecodes/data/example_chr2_spleen/cuLnrows.txt new file mode 100644 index 00000000..fff0a247 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLnrows.txt @@ -0,0 +1 @@ +74 diff --git a/sourcecodes/data/example_chr2_spleen/cuLparent.txt b/sourcecodes/data/example_chr2_spleen/cuLparent.txt new file mode 100644 index 00000000..b8626c4c --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLparent.txt @@ -0,0 +1 @@ +4 diff --git a/sourcecodes/data/example_chr2_spleen/cuLrun_evidencemodified.sh b/sourcecodes/data/example_chr2_spleen/cuLrun_evidencemodified.sh new file mode 100644 index 00000000..5a228612 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLrun_evidencemodified.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}"/evidencemodified cuL +fi +exit diff --git a/sourcecodes/data/example_chr2_spleen/cuLrun_initialstructure.sh b/sourcecodes/data/example_chr2_spleen/cuLrun_initialstructure.sh new file mode 100644 index 00000000..1d0835a4 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLrun_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 cuL +fi +exit diff --git a/sourcecodes/data/example_chr2_spleen/cuLstructure_input.txt b/sourcecodes/data/example_chr2_spleen/cuLstructure_input.txt new file mode 100644 index 00000000..48837c69 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLstructure_input.txt @@ -0,0 +1,15 @@ +rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 +0 0 0 1 1 0 0 0 0 1 0 1 0 1 +0 0 0 0 0 0 0 0 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 1 0 0 1 1 1 1 0 0 +0 0 0 0 0 0 1 0 0 0 1 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 0 1 0 +0 0 0 0 0 0 1 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 1 0 0 1 0 0 0 0 0 +0 0 1 0 0 0 0 1 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 0 0 0 +0 0 1 1 1 0 1 0 0 1 1 0 0 0 diff --git a/sourcecodes/data/example_chr2_spleen/cuLstructure_input_temp.txt b/sourcecodes/data/example_chr2_spleen/cuLstructure_input_temp.txt new file mode 100644 index 00000000..f3589770 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLstructure_input_temp.txt @@ -0,0 +1,15 @@ +rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 +0.000000 0.808614 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.250558 1.000000 0.000000 0.960922 0.000000 1.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.596398 0.000000 0.786929 0.055837 0.000000 0.000000 0.590731 0.000000 0.000000 +0.000000 0.942409 0.000000 0.000000 0.000000 0.018121 0.000000 0.000000 0.000000 0.409269 0.000000 0.401871 0.000000 0.000000 +0.000000 0.590731 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.018396 0.000000 +0.000000 0.038935 0.000000 0.500000 0.000000 0.036744 1.000000 0.000000 0.000000 0.000000 1.000000 0.039078 1.000000 0.000000 +0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.786929 0.164752 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 +0.000000 0.056298 0.000000 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a/sourcecodes/data/example_chr2_spleen/cuLstructure_old.txt b/sourcecodes/data/example_chr2_spleen/cuLstructure_old.txt new file mode 100644 index 00000000..f0815c7a --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLstructure_old.txt @@ -0,0 +1,14 @@ +rs3664317 0.5479 0.4521 +Dhx58 0.0024 0.0029 0.0035 0.0043 0.0053 0.0064 0.0076 0.0092 0.0110 0.0130 0.0154 0.0182 0.0213 0.0249 0.0290 0.0336 0.0388 0.0446 0.0510 0.0581 0.0659 0.0745 0.0838 0.0938 0.1046 0.1162 0.1284 0.1414 0.1550 0.1692 0.1839 0.1990 0.2145 0.2302 0.2459 0.2617 0.2772 0.2924 0.3071 0.3212 0.3346 0.3469 0.3582 0.3683 0.3771 0.3844 0.3902 0.3944 0.3970 0.3978 0.3970 0.3944 0.3902 0.3845 0.3771 0.3684 0.3583 0.3470 0.3346 0.3213 0.3072 0.2925 0.2773 0.2617 0.2460 0.2302 0.2146 0.1991 0.1840 0.1693 0.1551 0.1415 0.1285 0.1162 0.1047 0.0939 0.0838 0.0745 0.0660 0.0582 0.0510 0.0446 0.0388 0.0337 0.0290 0.0250 0.0213 0.0182 0.0154 0.0130 0.0110 0.0092 0.0077 0.0064 0.0053 0.0043 0.0035 0.0029 0.0024 0.0019 0.0015 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0.1112 0.1222 0.1337 0.1458 0.1585 0.1716 0.1851 0.1990 0.2132 0.2276 0.2420 0.2565 0.2709 0.2850 0.2988 0.3121 0.3249 0.3369 0.3482 0.3586 0.3679 0.3761 0.3832 0.3889 0.3934 0.3964 0.3981 0.3983 0.3971 0.3945 0.3905 0.3851 0.3785 0.3706 0.3617 0.3516 0.3406 0.3288 0.3163 0.3031 0.2894 0.2754 0.2611 0.2467 0.2322 0.2178 0.2035 0.1895 0.1759 0.1626 0.1498 0.1375 0.1258 0.1146 0.1041 0.0942 0.0849 0.0763 0.0683 0.0609 0.0541 0.0480 0.0423 0.0372 0.0326 0.0285 0.0247 0.0214 0.0185 0.0159 0.0137 0.0117 0.0099 0.0084 0.0071 0.0060 0.0050 0.0042 0.0035 0.0029 0.0024 +Oas1a 0.0034 0.0042 0.0051 0.0061 0.0073 0.0087 0.0104 0.0124 0.0146 0.0172 0.0201 0.0235 0.0273 0.0316 0.0364 0.0417 0.0477 0.0543 0.0616 0.0695 0.0782 0.0876 0.0977 0.1085 0.1201 0.1323 0.1452 0.1586 0.1727 0.1871 0.2020 0.2172 0.2325 0.2479 0.2633 0.2785 0.2933 0.3077 0.3214 0.3344 0.3465 0.3576 0.3675 0.3761 0.3834 0.3892 0.3935 0.3963 0.3974 0.3969 0.3947 0.3910 0.3857 0.3790 0.3708 0.3613 0.3507 0.3389 0.3263 0.3128 0.2986 0.2839 0.2689 0.2536 0.2382 0.2228 0.2075 0.1925 0.1779 0.1637 0.1500 0.1369 0.1245 0.1127 0.1016 0.0912 0.0816 0.0726 0.0644 0.0569 0.0501 0.0439 0.0383 0.0332 0.0288 0.0248 0.0213 0.0182 0.0155 0.0131 0.0111 0.0093 0.0078 0.0065 0.0054 0.0045 0.0037 0.0030 0.0025 0.0020 0.0016 +Irf7 0.0002 0.0003 0.0004 0.0005 0.0006 0.0008 0.0010 0.0013 0.0016 0.0021 0.0026 0.0033 0.0040 0.0050 0.0061 0.0075 0.0091 0.0111 0.0133 0.0160 0.0191 0.0226 0.0267 0.0314 0.0367 0.0428 0.0495 0.0570 0.0654 0.0746 0.0846 0.0956 0.1074 0.1201 0.1336 0.1478 0.1628 0.1784 0.1946 0.2111 0.2279 0.2448 0.2617 0.2783 0.2946 0.3102 0.3250 0.3388 0.3514 0.3627 0.3725 0.3806 0.3870 0.3916 0.3942 0.3948 0.3935 0.3903 0.3851 0.3781 0.3694 0.3591 0.3473 0.3343 0.3201 0.3050 0.2892 0.2728 0.2561 0.2392 0.2223 0.2056 0.1891 0.1732 0.1577 0.1430 0.1290 0.1157 0.1033 0.0918 0.0812 0.0714 0.0625 0.0544 0.0472 0.0407 0.0349 0.0298 0.0253 0.0214 0.0180 0.0151 0.0125 0.0104 0.0086 0.0070 0.0057 0.0047 0.0038 0.0030 0.0024 +Mx1 0.0028 0.0035 0.0043 0.0053 0.0066 0.0081 0.0098 0.0119 0.0144 0.0173 0.0207 0.0246 0.0291 0.0342 0.0400 0.0465 0.0539 0.0621 0.0711 0.0811 0.0919 0.1037 0.1164 0.1300 0.1444 0.1595 0.1754 0.1918 0.2086 0.2258 0.2431 0.2604 0.2775 0.2941 0.3102 0.3254 0.3396 0.3526 0.3641 0.3742 0.3824 0.3889 0.3934 0.3959 0.3964 0.3948 0.3911 0.3855 0.3780 0.3688 0.3579 0.3455 0.3318 0.3170 0.3013 0.2849 0.2680 0.2508 0.2335 0.2162 0.1992 0.1826 0.1665 0.1510 0.1363 0.1223 0.1092 0.0970 0.0858 0.0754 0.0660 0.0574 0.0497 0.0428 0.0367 0.0312 0.0265 0.0223 0.0187 0.0156 0.0130 0.0107 0.0088 0.0072 0.0059 0.0047 0.0038 0.0031 0.0024 0.0019 0.0015 0.0012 0.0009 0.0007 0.0006 0.0004 0.0003 0.0002 0.0002 0.0001 0.0001 +Trim25 0.0009 0.0012 0.0014 0.0018 0.0022 0.0026 0.0032 0.0039 0.0047 0.0056 0.0068 0.0081 0.0096 0.0113 0.0133 0.0156 0.0183 0.0213 0.0247 0.0286 0.0329 0.0377 0.0431 0.0490 0.0556 0.0628 0.0706 0.0791 0.0883 0.0982 0.1087 0.1200 0.1319 0.1444 0.1575 0.1711 0.1851 0.1996 0.2144 0.2293 0.2444 0.2594 0.2743 0.2889 0.3031 0.3168 0.3299 0.3422 0.3535 0.3638 0.3730 0.3809 0.3875 0.3927 0.3964 0.3987 0.3993 0.3985 0.3961 0.3922 0.3868 0.3801 0.3720 0.3627 0.3522 0.3408 0.3284 0.3153 0.3015 0.2872 0.2725 0.2576 0.2426 0.2275 0.2126 0.1979 0.1835 0.1695 0.1559 0.1429 0.1304 0.1186 0.1075 0.0970 0.0872 0.0781 0.0696 0.0619 0.0548 0.0483 0.0424 0.0371 0.0323 0.0281 0.0243 0.0209 0.0180 0.0153 0.0131 0.0111 0.0094 +Oas3 0.0017 0.0021 0.0026 0.0032 0.0039 0.0048 0.0059 0.0072 0.0087 0.0104 0.0125 0.0149 0.0177 0.0209 0.0246 0.0289 0.0337 0.0391 0.0452 0.0520 0.0595 0.0679 0.0771 0.0871 0.0980 0.1098 0.1224 0.1358 0.1501 0.1651 0.1808 0.1971 0.2139 0.2311 0.2486 0.2662 0.2837 0.3011 0.3181 0.3345 0.3502 0.3650 0.3787 0.3911 0.4021 0.4116 0.4195 0.4255 0.4297 0.4320 0.4324 0.4308 0.4273 0.4220 0.4148 0.4059 0.3954 0.3835 0.3702 0.3558 0.3405 0.3243 0.3075 0.2903 0.2728 0.2552 0.2377 0.2204 0.2034 0.1869 0.1709 0.1557 0.1411 0.1273 0.1144 0.1023 0.0911 0.0807 0.0712 0.0626 0.0547 0.0476 0.0413 0.0356 0.0306 0.0262 0.0223 0.0189 0.0159 0.0134 0.0112 0.0093 0.0077 0.0064 0.0052 0.0043 0.0035 0.0028 0.0023 0.0018 0.0015 +Pglyrp3 0.0011 0.0014 0.0017 0.0021 0.0026 0.0032 0.0039 0.0047 0.0057 0.0069 0.0083 0.0100 0.0119 0.0141 0.0166 0.0196 0.0229 0.0267 0.0310 0.0359 0.0413 0.0474 0.0541 0.0614 0.0695 0.0783 0.0878 0.0981 0.1091 0.1208 0.1332 0.1462 0.1598 0.1739 0.1885 0.2034 0.2185 0.2337 0.2490 0.2640 0.2788 0.2931 0.3069 0.3199 0.3320 0.3431 0.3530 0.3617 0.3690 0.3748 0.3790 0.3817 0.3827 0.3821 0.3798 0.3759 0.3705 0.3635 0.3552 0.3455 0.3347 0.3228 0.3100 0.2964 0.2822 0.2675 0.2525 0.2373 0.2220 0.2069 0.1919 0.1773 0.1631 0.1493 0.1362 0.1236 0.1118 0.1006 0.0902 0.0804 0.0715 0.0632 0.0557 0.0489 0.0427 0.0371 0.0321 0.0277 0.0238 0.0203 0.0173 0.0147 0.0124 0.0104 0.0087 0.0072 0.0060 0.0050 0.0041 0.0033 0.0027 +Pml 0.0001 0.0001 0.0002 0.0002 0.0003 0.0004 0.0005 0.0006 0.0008 0.0010 0.0013 0.0016 0.0020 0.0026 0.0032 0.0040 0.0049 0.0060 0.0073 0.0089 0.0107 0.0129 0.0154 0.0184 0.0218 0.0257 0.0302 0.0353 0.0411 0.0476 0.0548 0.0628 0.0716 0.0813 0.0918 0.1032 0.1155 0.1285 0.1424 0.1570 0.1722 0.1880 0.2043 0.2209 0.2377 0.2546 0.2713 0.2877 0.3036 0.3188 0.3332 0.3466 0.3587 0.3695 0.3787 0.3863 0.3922 0.3962 0.3983 0.3985 0.3967 0.3930 0.3875 0.3802 0.3713 0.3608 0.3489 0.3357 0.3215 0.3064 0.2906 0.2743 0.2576 0.2408 0.2240 0.2073 0.1910 0.1751 0.1597 0.1450 0.1310 0.1178 0.1054 0.0938 0.0831 0.0733 0.0643 0.0562 0.0488 0.0422 0.0363 0.0311 0.0265 0.0225 0.0190 0.0159 0.0133 0.0111 0.0092 0.0076 0.0062 diff --git a/sourcecodes/data/example_chr2_spleen/cuLthr.txt b/sourcecodes/data/example_chr2_spleen/cuLthr.txt new file mode 100644 index 00000000..b63ba696 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLthr.txt @@ -0,0 +1 @@ +0.9 diff --git a/sourcecodes/data/example_chr2_spleen/cuLtier.txt b/sourcecodes/data/example_chr2_spleen/cuLtier.txt new file mode 100644 index 00000000..e71cfdda --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLtier.txt @@ -0,0 +1 @@ +3,Tier1,1,rs3664317,Tier2,1,Ifih1,Tier3,12,Oas1a,Parp9,Dhx58,Cd1d1,Irf7,Oas3,Pml,Mx1,Ifit1,Trim25,Oas1g,Pglyrp3, \ No newline at end of file diff --git a/sourcecodes/data/example_chr2_spleen/cuLtype.txt b/sourcecodes/data/example_chr2_spleen/cuLtype.txt new file mode 100644 index 00000000..1b707710 --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLtype.txt @@ -0,0 +1,2 @@ +rs3664317 Oas1a Parp9 Dhx58 Cd1d1 Irf7 Oas3 Pml Mx1 Ifit1 Trim25 Oas1g Pglyrp3 Ifih1 +2 1 1 1 1 1 1 1 1 1 1 1 1 1 diff --git a/sourcecodes/data/example_chr2_spleen/cuLwhite.txt b/sourcecodes/data/example_chr2_spleen/cuLwhite.txt new file mode 100644 index 00000000..83e81b8b --- /dev/null +++ b/sourcecodes/data/example_chr2_spleen/cuLwhite.txt @@ -0,0 +1 @@ +From To |