[Genabel-commits] r1735 - in pkg/ProbABEL: checks/inputfiles checks/verified_results doc src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon May 19 22:24:53 CEST 2014
Author: lckarssen
Date: 2014-05-19 22:24:52 +0200 (Mon, 19 May 2014)
New Revision: 1735
Modified:
pkg/ProbABEL/checks/inputfiles/test.mldose
pkg/ProbABEL/checks/verified_results/height_add.out.txt
pkg/ProbABEL/checks/verified_results/height_base_add.out.txt
pkg/ProbABEL/checks/verified_results/height_ngp2_2df.out.txt
pkg/ProbABEL/checks/verified_results/height_ngp2_add.out.txt
pkg/ProbABEL/checks/verified_results/height_ngp2_domin.out.txt
pkg/ProbABEL/checks/verified_results/height_ngp2_over_domin.out.txt
pkg/ProbABEL/checks/verified_results/height_ngp2_recess.out.txt
pkg/ProbABEL/doc/ChangeLog
pkg/ProbABEL/src/coxph_data.cpp
pkg/ProbABEL/src/main.cpp
Log:
Changed the way ProbABEL prints not-a-numbers in its output from "nan" to "NaN", which is more common (and maybe the way IEEE 754 specifies it, see the forum message http://forum.genabel.org/viewtopic.php?f=10&t=879#p1840).
Modified: pkg/ProbABEL/checks/inputfiles/test.mldose
===================================================================
--- pkg/ProbABEL/checks/inputfiles/test.mldose 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/checks/inputfiles/test.mldose 2014-05-19 20:24:52 UTC (rev 1735)
@@ -1,200 +1,200 @@
1->id636728 MLDOSE 0.678 1.622 1.732 1.585 1.867 1.000
-2->id890314 MLDOSE 0.66 1.621 1.737 1.59 1.869 2.000
+2->id890314 MLDOSE 0.660 1.621 1.737 1.590 1.869 2.000
3->id102874 MLDOSE 0.684 1.623 1.731 1.585 1.866 2.000
-4->id200949 MLDOSE 0.667 NaN 1.728 1.576 1.866 2.000
-5->id336491 MLDOSE 0.66 1.609 1.737 1.577 1.869 2.000
-6->id988766 MLDOSE 0.687 1.622 1.738 1.59 1.868 2.000
-7->id21999 MLDOSE 0.67 1.62 1.735 1.588 1.867 2.000
+4->id200949 MLDOSE 0.667 NaN 1.728 1.576 1.866 2.000
+5->id336491 MLDOSE 0.660 1.609 1.737 1.577 1.869 2.000
+6->id988766 MLDOSE 0.687 1.622 1.738 1.590 1.868 2.000
+7->id21999 MLDOSE 0.670 1.620 1.735 1.588 1.867 2.000
8->id433893 MLDOSE 0.663 1.615 1.734 1.572 1.869 2.000
9->id688932 MLDOSE 0.672 1.619 1.729 1.585 1.862 2.000
-10->id394203 MLDOSE 0.666 1.619 1.729 1.58 1.863 2.000
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11->id995678 MLDOSE 0.672 1.619 1.733 1.583 1.867 2.000
-12->id694339 MLDOSE 0.666 1.615 1.733 1.59 1.869 2.000
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13->id256455 MLDOSE 0.673 1.617 1.737 1.584 1.869 2.000
-14->id14836 MLDOSE 0.672 1.62 1.737 1.582 1.869 2.000
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15->id817128 MLDOSE 0.666 1.609 1.735 1.589 1.868 2.000
-16->id803325 MLDOSE 0.678 1.62 1.73 1.591 1.868 2.000
-17->id521287 MLDOSE 0.661 1.618 1.736 1.585 1.87 2.000
+16->id803325 MLDOSE 0.678 1.620 1.730 1.591 1.868 2.000
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18->id701472 MLDOSE 0.666 1.621 1.731 1.585 1.867 2.000
19->id850010 MLDOSE 0.669 1.615 1.736 1.581 1.868 2.000
20->id268483 MLDOSE 0.669 1.618 1.732 1.582 1.865 2.000
-21->id738781 MLDOSE 0.666 1.611 1.73 1.59 1.862 2.000
-22->id28411 MLDOSE 0.66 1.62 1.735 1.57 1.869 2.000
+21->id738781 MLDOSE 0.666 1.611 1.730 1.590 1.862 2.000
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23->id541635 MLDOSE 0.669 1.622 1.725 1.558 1.868 2.000
24->id751101 MLDOSE 0.669 1.624 1.738 1.589 1.869 2.000
25->id826300 MLDOSE 0.666 1.605 1.736 1.586 1.869 2.000
26->id884387 MLDOSE 0.661 1.604 1.734 1.587 1.868 2.000
27->id492414 MLDOSE 0.666 1.619 1.733 1.583 1.866 2.000
28->id268871 MLDOSE 0.669 1.621 1.731 1.576 1.869 2.000
-29->id627354 MLDOSE 0.666 1.615 1.735 1.59 1.869 2.000
-30->id503932 MLDOSE 0.66 1.62 1.735 1.586 1.867 2.000
+29->id627354 MLDOSE 0.666 1.615 1.735 1.590 1.869 2.000
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31->id163442 MLDOSE 0.675 1.621 1.737 1.586 1.869 2.000
-32->id317797 MLDOSE 0.654 1.625 1.739 1.57 1.87 2.000
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33->id687857 MLDOSE 0.667 1.621 1.734 1.586 1.869 2.000
-34->id871570 MLDOSE 0.666 1.61 1.731 1.576 1.864 2.000
+34->id871570 MLDOSE 0.666 1.610 1.731 1.576 1.864 2.000
35->id724067 MLDOSE 0.666 1.619 1.736 1.583 1.868 2.000
36->id874076 MLDOSE 0.676 1.617 1.738 1.585 1.869 2.000
-37->id927863 MLDOSE 0.67 1.62 1.734 1.586 1.865 2.000
-38->id369805 MLDOSE 0.663 1.616 1.73 1.583 1.867 2.000
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39->id668376 MLDOSE 0.675 1.617 1.736 1.582 1.869 2.000
-40->id717362 MLDOSE 0.66 1.62 1.736 1.59 1.869 2.000
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41->id665504 MLDOSE 0.669 1.618 1.732 1.578 1.867 2.000
42->id336637 MLDOSE 0.661 1.618 1.734 1.576 1.865 2.000
43->id60633 MLDOSE 0.669 1.619 1.731 1.579 1.866 2.000
44->id848600 MLDOSE 0.664 1.615 1.737 1.576 1.869 2.000
45->id169514 MLDOSE 0.664 1.615 1.737 1.583 1.869 2.000
46->id690732 MLDOSE 0.663 1.619 1.737 1.586 1.868 2.000
-47->id684760 MLDOSE 0.667 1.62 1.734 1.578 1.866 2.000
-48->id553502 MLDOSE 0.672 1.608 1.732 1.59 1.869 2.000
+47->id684760 MLDOSE 0.667 1.620 1.734 1.578 1.866 2.000
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49->id214917 MLDOSE 0.669 1.618 1.727 1.588 1.865 2.000
50->id849169 MLDOSE 0.664 1.624 1.733 1.588 1.867 2.000
51->id941921 MLDOSE 0.667 1.619 1.731 1.588 1.862 2.000
-52->id784646 MLDOSE 0.663 1.603 1.739 1.584 1.87 2.000
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53->id520954 MLDOSE 0.664 1.619 1.732 1.581 1.864 2.000
-54->id996355 MLDOSE 0.66 1.605 1.736 1.586 1.865 2.000
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55->id96730 MLDOSE 0.664 1.619 1.736 1.573 1.868 2.000
56->id673442 MLDOSE 0.666 1.609 1.735 1.575 1.867 2.000
57->id68305 MLDOSE 0.672 1.618 1.735 1.585 1.866 2.000
58->id653025 MLDOSE 0.678 1.617 1.738 1.585 1.868 2.000
-59->id208543 MLDOSE 0.664 1.618 1.734 1.58 1.868 2.000
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60->id335725 MLDOSE 0.666 1.616 1.714 1.593 1.845 2.000
61->id980400 MLDOSE 0.663 1.607 1.733 1.588 1.867 2.000
62->id869939 MLDOSE 0.667 1.619 1.733 1.588 1.865 2.000
-63->id297563 MLDOSE 0.673 1.614 1.72 1.585 1.866 2.000
-64->id852663 MLDOSE 0.666 1.603 1.729 1.585 1.87 2.000
+63->id297563 MLDOSE 0.673 1.614 1.720 1.585 1.866 2.000
+64->id852663 MLDOSE 0.666 1.603 1.729 1.585 1.870 2.000
65->id162070 MLDOSE 0.666 1.619 1.728 1.572 1.868 2.000
-66->id272875 MLDOSE 0.66 1.605 1.737 1.584 1.869 2.000
-67->id163787 MLDOSE 0.661 1.616 1.723 1.584 1.87 2.000
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+67->id163787 MLDOSE 0.661 1.616 1.723 1.584 1.870 2.000
68->id422204 MLDOSE 0.663 1.615 1.734 1.576 1.867 2.000
-69->id120197 MLDOSE 0.66 1.62 1.731 1.588 1.87 2.000
-70->id33660 MLDOSE 0.658 1.62 1.736 1.571 1.869 2.000
+69->id120197 MLDOSE 0.660 1.620 1.731 1.588 1.870 2.000
+70->id33660 MLDOSE 0.658 1.620 1.736 1.571 1.869 2.000
71->id803855 MLDOSE 0.669 1.616 1.732 1.586 1.865 2.000
72->id255048 MLDOSE 0.675 1.616 1.726 1.582 1.866 2.000
-73->id690936 MLDOSE 0.657 1.588 1.738 1.59 1.87 2.000
+73->id690936 MLDOSE 0.657 1.588 1.738 1.590 1.870 2.000
74->id126807 MLDOSE 0.667 1.612 1.731 1.589 1.864 2.000
-75->id99016 MLDOSE 0.667 1.612 1.734 1.59 1.864 2.000
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76->id883847 MLDOSE 0.666 1.611 1.736 1.587 1.869 2.000
-77->id354523 MLDOSE 0.669 1.62 1.734 1.584 1.868 2.000
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78->id737255 MLDOSE 0.666 1.623 1.733 1.569 1.867 2.000
-79->id990941 MLDOSE 0.675 1.62 1.734 1.585 1.869 2.000
-80->id25464 MLDOSE 0.673 1.62 1.737 1.579 1.868 2.000
-81->id918375 MLDOSE 0.672 1.621 1.737 1.58 1.869 2.000
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82->id537828 MLDOSE 0.666 1.613 1.729 1.585 1.869 2.000
83->id682778 MLDOSE 0.658 1.621 1.737 1.573 1.869 2.000
-84->id587547 MLDOSE 0.669 1.62 1.738 1.585 1.868 2.000
-85->id670874 MLDOSE 0.666 1.618 1.734 1.58 1.867 2.000
-86->id444459 MLDOSE 0.66 1.617 1.734 1.577 1.87 2.000
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87->id777456 MLDOSE 0.663 1.615 1.732 1.581 1.865 2.000
88->id452384 MLDOSE 0.666 1.625 1.738 1.588 1.869 2.000
89->id826975 MLDOSE 0.669 1.619 1.731 1.582 1.865 2.000
-90->id519567 MLDOSE 0.66 1.621 1.732 1.586 1.869 2.000
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91->id84292 MLDOSE 0.663 1.618 1.737 1.582 1.868 2.000
92->id124432 MLDOSE 0.684 1.621 1.736 1.591 1.867 2.000
93->id800145 MLDOSE 0.681 1.621 1.737 1.587 1.869 2.000
-94->id153857 MLDOSE 0.661 1.617 1.739 1.585 1.87 2.000
+94->id153857 MLDOSE 0.661 1.617 1.739 1.585 1.870 2.000
95->id587157 MLDOSE 0.663 1.619 1.736 1.584 1.866 2.000
96->id506262 MLDOSE 0.664 1.613 1.719 1.592 1.855 2.000
97->id634462 MLDOSE 0.673 1.623 1.737 1.585 1.869 2.000
98->id687592 MLDOSE 0.664 1.615 1.726 1.584 1.869 2.000
99->id955526 MLDOSE 0.663 1.621 1.737 1.566 1.869 2.000
-100->id181850 MLDOSE 0.66 1.603 1.736 1.586 1.869 2.000
+100->id181850 MLDOSE 0.660 1.603 1.736 1.586 1.869 2.000
101->id159506 MLDOSE 0.667 1.621 1.735 1.585 1.868 2.000
-102->id609051 MLDOSE 0.675 1.618 1.73 1.59 1.86 2.000
-103->id963886 MLDOSE 0.663 1.612 1.739 1.581 1.87 2.000
+102->id609051 MLDOSE 0.675 1.618 1.730 1.590 1.860 2.000
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104->id405792 MLDOSE 0.682 1.621 1.737 1.589 1.869 2.000
-105->id494172 MLDOSE 0.66 1.607 1.736 1.58 1.868 2.000
-106->id964637 MLDOSE 0.663 1.616 1.73 1.59 1.861 2.000
-107->id799355 MLDOSE 0.669 1.62 1.735 1.585 1.868 2.000
-108->id157111 MLDOSE 0.658 1.601 1.731 1.588 1.87 2.000
-109->id114524 MLDOSE 0.666 1.603 1.729 1.585 1.87 2.000
-110->id954931 MLDOSE 0.676 1.62 1.733 1.585 1.868 2.000
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111->id827034 MLDOSE 0.664 1.613 1.737 1.579 1.869 2.000
-112->id689645 MLDOSE 0.657 1.611 1.736 1.59 1.868 2.000
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113->id281585 MLDOSE 0.673 1.621 1.736 1.584 1.869 2.000
114->id885624 MLDOSE 0.672 1.619 1.734 1.585 1.869 2.000
-115->id577871 MLDOSE 0.67 1.616 1.731 1.585 1.864 2.000
-116->id238796 MLDOSE 0.667 1.62 1.734 1.585 1.867 2.000
-117->id481035 MLDOSE 0.664 1.62 1.737 1.588 1.867 2.000
-118->id972713 MLDOSE 0.666 1.611 1.73 1.589 1.869 2.000
-119->id905484 MLDOSE 0.66 1.62 1.728 1.572 1.869 2.000
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120->id713511 MLDOSE 0.664 1.605 1.733 1.585 1.866 2.000
-121->id512328 MLDOSE 0.67 1.616 1.737 1.584 1.869 2.000
-122->id703534 MLDOSE 0.67 1.615 1.731 1.59 1.862 2.000
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123->id409904 MLDOSE 0.678 1.622 1.734 1.585 1.868 2.000
124->id577169 MLDOSE 0.669 1.616 1.734 1.582 1.867 2.000
-125->id813971 MLDOSE 0.657 1.606 1.72 1.591 1.85 2.000
-126->id558483 MLDOSE 0.669 1.62 1.737 1.59 1.868 2.000
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127->id892784 MLDOSE 0.669 1.621 1.733 1.586 1.866 2.000
128->id611178 MLDOSE 0.666 1.611 1.735 1.582 1.866 2.000
-129->id192732 MLDOSE 0.666 1.618 1.735 1.59 1.868 2.000
-130->id917280 MLDOSE 0.66 1.602 1.736 1.567 1.869 2.000
-131->id435876 MLDOSE 0.678 1.619 1.739 1.586 1.87 2.000
-132->id980722 MLDOSE 0.663 1.62 1.735 1.572 1.869 2.000
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133->id308273 MLDOSE 0.661 1.617 1.737 1.582 1.868 2.000
134->id476685 MLDOSE 0.675 1.618 1.733 1.584 1.867 2.000
135->id315883 MLDOSE 0.669 1.612 1.736 1.573 1.869 2.000
-136->id935945 MLDOSE 0.663 1.614 1.733 1.58 1.865 2.000
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137->id991781 MLDOSE 0.664 1.614 1.731 1.586 1.864 2.000
138->id65199 MLDOSE 0.661 1.619 1.731 1.575 1.869 2.000
-139->id226233 MLDOSE 0.661 1.618 1.724 1.59 1.854 2.000
-140->id860183 MLDOSE 0.66 1.609 1.734 1.577 1.866 2.000
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141->id295209 MLDOSE 0.669 1.614 1.735 1.585 1.867 2.000
142->id544964 MLDOSE 0.669 1.619 1.732 1.582 1.868 2.000
143->id648663 MLDOSE 0.666 1.617 1.734 1.585 1.868 2.000
144->id710165 MLDOSE 0.666 1.615 1.728 1.585 1.869 2.000
145->id392593 MLDOSE 0.666 1.621 1.738 1.569 1.868 2.000
-146->id129945 MLDOSE 0.66 1.62 1.733 1.587 1.869 2.000
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147->id382621 MLDOSE 0.684 1.621 1.736 1.591 1.867 2.000
-148->id901440 MLDOSE 0.661 1.615 1.718 1.59 1.852 2.000
-149->id39847 MLDOSE 0.669 1.619 1.729 1.58 1.863 2.000
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150->id526460 MLDOSE 0.664 1.614 1.731 1.586 1.863 2.000
-151->id477473 MLDOSE 0.672 1.619 1.73 1.589 1.862 2.000
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152->id448194 MLDOSE 0.669 1.614 1.737 1.586 1.868 2.000
-153->id904184 MLDOSE 0.67 1.618 1.73 1.577 1.868 2.000
-154->id747852 MLDOSE 0.664 1.615 1.73 1.578 1.869 2.000
+153->id904184 MLDOSE 0.670 1.618 1.730 1.577 1.868 2.000
+154->id747852 MLDOSE 0.664 1.615 1.730 1.578 1.869 2.000
155->id711012 MLDOSE 0.672 1.605 1.736 1.575 1.868 2.000
156->id683879 MLDOSE 0.672 1.619 1.734 1.588 1.867 2.000
157->id789575 MLDOSE 0.658 1.618 1.733 1.591 1.863 2.000
158->id650729 MLDOSE 0.676 1.615 1.733 1.589 1.867 2.000
-159->id934302 MLDOSE 0.66 1.62 1.733 1.581 1.866 2.000
+159->id934302 MLDOSE 0.660 1.620 1.733 1.581 1.866 2.000
160->id555013 MLDOSE 0.667 1.622 1.731 1.574 1.865 2.000
-161->id82779 MLDOSE 0.675 1.618 1.73 1.585 1.867 2.000
+161->id82779 MLDOSE 0.675 1.618 1.730 1.585 1.867 2.000
162->id771444 MLDOSE 0.669 1.616 1.718 1.592 1.856 2.000
-163->id821562 MLDOSE 0.675 1.625 1.739 1.58 1.87 2.000
-164->id292809 MLDOSE 0.66 1.614 1.731 1.58 1.869 2.000
+163->id821562 MLDOSE 0.675 1.625 1.739 1.580 1.870 2.000
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165->id645690 MLDOSE 0.684 1.624 1.733 1.586 1.867 2.000
166->id223901 MLDOSE 0.666 1.615 1.733 1.576 1.868 2.000
167->id41320 MLDOSE 0.661 1.617 1.732 1.576 1.869 2.000
168->id96181 MLDOSE 0.684 1.621 1.716 1.593 1.867 2.000
169->id147900 MLDOSE 0.658 1.603 1.738 1.577 1.868 2.000
-170->id702917 MLDOSE 0.669 1.614 1.731 1.59 1.864 2.000
+170->id702917 MLDOSE 0.669 1.614 1.731 1.590 1.864 2.000
171->id150640 MLDOSE 0.669 1.621 1.734 1.583 1.868 2.000
-172->id518391 MLDOSE 0.66 1.62 1.736 1.589 1.869 2.000
+172->id518391 MLDOSE 0.660 1.620 1.736 1.589 1.869 2.000
173->id879076 MLDOSE 0.661 1.613 1.738 1.573 1.868 2.000
-174->id952031 MLDOSE 0.66 1.621 1.734 1.58 1.866 2.000
-175->id10055 MLDOSE 0.67 1.611 1.732 1.589 1.866 2.000
+174->id952031 MLDOSE 0.660 1.621 1.734 1.580 1.866 2.000
+175->id10055 MLDOSE 0.670 1.611 1.732 1.589 1.866 2.000
176->id727213 MLDOSE 0.664 1.622 1.733 1.583 1.869 2.000
-177->id41961 MLDOSE 0.66 1.62 1.737 1.572 1.867 2.000
+177->id41961 MLDOSE 0.660 1.620 1.737 1.572 1.867 2.000
178->id257209 MLDOSE 0.673 1.616 1.736 1.588 1.869 2.000
-179->id995361 MLDOSE 0.661 1.62 1.723 1.571 1.868 2.000
+179->id995361 MLDOSE 0.661 1.620 1.723 1.571 1.868 2.000
180->id957918 MLDOSE 0.663 1.618 1.726 1.581 1.869 2.000
-181->id975370 MLDOSE 0.67 1.614 1.738 1.583 1.87 2.000
+181->id975370 MLDOSE 0.670 1.614 1.738 1.583 1.870 2.000
182->id889896 MLDOSE 0.679 1.618 1.733 1.589 1.869 2.000
-183->id978164 MLDOSE 0.669 1.62 1.735 1.586 1.868 2.000
-184->id90359 MLDOSE 0.675 1.621 1.737 1.58 1.869 2.000
-185->id307158 MLDOSE 0.675 1.615 1.71 1.591 1.86 2.000
+183->id978164 MLDOSE 0.669 1.620 1.735 1.586 1.868 2.000
+184->id90359 MLDOSE 0.675 1.621 1.737 1.580 1.869 2.000
+185->id307158 MLDOSE 0.675 1.615 1.710 1.591 1.860 2.000
186->id755940 MLDOSE 0.669 1.618 1.734 1.577 1.869 2.000
187->id995582 MLDOSE 0.666 1.615 1.724 1.591 1.853 2.000
188->id363965 MLDOSE 0.663 1.619 1.736 1.574 1.868 2.000
-189->id729124 MLDOSE 0.666 1.611 1.73 1.587 1.86 2.000
-190->id871963 MLDOSE 0.67 1.62 1.737 1.585 1.868 2.000
+189->id729124 MLDOSE 0.666 1.611 1.730 1.587 1.860 2.000
+190->id871963 MLDOSE 0.670 1.620 1.737 1.585 1.868 2.000
191->id475172 MLDOSE 0.663 1.621 1.737 1.579 1.869 2.000
192->id804699 MLDOSE 0.663 1.619 1.731 1.581 1.868 2.000
-193->id625843 MLDOSE 0.667 1.622 1.738 1.583 1.87 2.000
+193->id625843 MLDOSE 0.667 1.622 1.738 1.583 1.870 2.000
194->id595713 MLDOSE 0.657 1.599 1.736 1.588 1.869 2.000
195->id462604 MLDOSE 0.663 1.616 1.731 1.584 1.867 2.000
196->id106141 MLDOSE 0.672 1.612 1.732 1.589 1.864 2.000
197->id689349 MLDOSE 0.666 1.609 1.738 1.583 1.869 2.000
-198->id639003 MLDOSE 0.672 1.618 1.728 1.58 1.863 2.000
-199->id393896 MLDOSE 0.663 1.617 1.73 1.579 1.868 2.000
-200->id450307 MLDOSE 0.663 1.622 1.739 1.588 1.87 2.000
+198->id639003 MLDOSE 0.672 1.618 1.728 1.580 1.863 2.000
+199->id393896 MLDOSE 0.663 1.617 1.730 1.579 1.868 2.000
+200->id450307 MLDOSE 0.663 1.622 1.739 1.588 1.870 2.000
Modified: pkg/ProbABEL/checks/verified_results/height_add.out.txt
===================================================================
--- pkg/ProbABEL/checks/verified_results/height_add.out.txt 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/checks/verified_results/height_add.out.txt 2014-05-19 20:24:52 UTC (rev 1735)
@@ -3,4 +3,4 @@
rs8102643 C TGGT 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -25.7632 86.4877 0.0907169
rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -40.7722 102.559 0.161525
rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 35.3602 81.7869 0.191023
-rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 nan nan nan
+rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 NaN NaN NaN
Modified: pkg/ProbABEL/checks/verified_results/height_base_add.out.txt
===================================================================
--- pkg/ProbABEL/checks/verified_results/height_base_add.out.txt 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/checks/verified_results/height_base_add.out.txt 2014-05-19 20:24:52 UTC (rev 1735)
@@ -3,5 +3,5 @@
rs8102643 C TGGT 0.5847 0.415 0.9308 0.8685 181 0.808177 19 207859 -25.7632 86.4877 0.0907169
rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 19 211970 -40.7722 102.559 0.161525
rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 19 212033 35.3602 81.7869 0.191023
-rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 19 217034 nan nan nan
+rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 19 217034 NaN NaN NaN
rs3174230 G C 0.8123 1.2e-05 0.9991 0.0185 182 0.997253 19 7845238 -6.73472 6.49041 1.09758
Modified: pkg/ProbABEL/checks/verified_results/height_ngp2_2df.out.txt
===================================================================
--- pkg/ProbABEL/checks/verified_results/height_ngp2_2df.out.txt 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/checks/verified_results/height_ngp2_2df.out.txt 2014-05-19 20:24:52 UTC (rev 1735)
@@ -3,4 +3,4 @@
rs8102643 C TGGT 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -820.466 1392.51 -646.111 1054.18 0.426657
rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -239.796 1308.51 -246.734 1102.07 0.185459
rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 782.482 1474.58 604.324 1064.24 0.45561
-rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 nan nan nan nan nan
+rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 NaN NaN NaN NaN NaN
Modified: pkg/ProbABEL/checks/verified_results/height_ngp2_add.out.txt
===================================================================
--- pkg/ProbABEL/checks/verified_results/height_ngp2_add.out.txt 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/checks/verified_results/height_ngp2_add.out.txt 2014-05-19 20:24:52 UTC (rev 1735)
@@ -3,4 +3,4 @@
rs8102643 C TGGT 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -25.7632 86.4877 0.0907169
rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -40.7722 102.559 0.161525
rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 35.3602 81.7869 0.191023
-rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 nan nan nan
+rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 NaN NaN NaN
Modified: pkg/ProbABEL/checks/verified_results/height_ngp2_domin.out.txt
===================================================================
--- pkg/ProbABEL/checks/verified_results/height_ngp2_domin.out.txt 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/checks/verified_results/height_ngp2_domin.out.txt 2014-05-19 20:24:52 UTC (rev 1735)
@@ -3,4 +3,4 @@
rs8102643 C TGGT 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -178.139 417.232 0.186313
rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -272.156 640.298 0.18463
rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 188.389 361.093 0.278093
-rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 nan nan nan
+rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 NaN NaN NaN
Modified: pkg/ProbABEL/checks/verified_results/height_ngp2_over_domin.out.txt
===================================================================
--- pkg/ProbABEL/checks/verified_results/height_ngp2_over_domin.out.txt 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/checks/verified_results/height_ngp2_over_domin.out.txt 2014-05-19 20:24:52 UTC (rev 1735)
@@ -3,4 +3,4 @@
rs8102643 C TGGT 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 28.4969 142.757 0.0407436
rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 51.4168 142.042 0.133927
rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 -50.7538 145.509 0.124354
-rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 nan nan nan
+rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 NaN NaN NaN
Modified: pkg/ProbABEL/checks/verified_results/height_ngp2_recess.out.txt
===================================================================
--- pkg/ProbABEL/checks/verified_results/height_ngp2_recess.out.txt 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/checks/verified_results/height_ngp2_recess.out.txt 2014-05-19 20:24:52 UTC (rev 1735)
@@ -3,4 +3,4 @@
rs8102643 C TGGT 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -28.2737 108.063 0.0699893
rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -45.9705 119.627 0.15093
rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 42.3577 105.005 0.166302
-rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 nan nan nan
+rs2312724 T C 0.9122 0.0877 0.9841 1.3e-17 182 0.933464 2 217034 NaN NaN NaN
Modified: pkg/ProbABEL/doc/ChangeLog
===================================================================
--- pkg/ProbABEL/doc/ChangeLog 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/doc/ChangeLog 2014-05-19 20:24:52 UTC (rev 1735)
@@ -1,7 +1,10 @@
***** v.0.5.0 (2014.)
* ProbABEL now depends on the Eigen library. The option to compile without
Eigen has been removed.
+* Not-a-number values in the output are now printed as "NaN" instead of
+ "nan".
+
***** v.0.4.3 (2014.04.01)
* Speed-up of a factor of ~ 2 for linear, logistic and Cox regression when
using filevector input files.
Modified: pkg/ProbABEL/src/coxph_data.cpp
===================================================================
--- pkg/ProbABEL/src/coxph_data.cpp 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/src/coxph_data.cpp 2014-05-19 20:24:52 UTC (rev 1735)
@@ -472,7 +472,7 @@
if (flag < X.nrow && niter > 0) {
cerr << "Warning for " << snpinfo.name[cursnp]
<< ": X matrix deemed to be singular,"
- << " setting beta and se to 'nan'\n";
+ << " setting beta and se to 'NaN'\n";
setToZero = true;
}
@@ -487,7 +487,7 @@
{
cerr << "Warning for " << snpinfo.name[cursnp]
<< ": Cox regression ran out of iterations and did not converge,"
- << " setting beta and se to 'nan'\n";
+ << " setting beta and se to 'NaN'\n";
setToZero = true;
} else {
VectorXd ueigen = u.data;
@@ -499,7 +499,7 @@
{
cerr << "Warning for " << snpinfo.name[cursnp]
<< ": beta may be infinite,"
- << " setting beta and se to 'nan'\n";
+ << " setting beta and se to 'NaN'\n";
setToZero = true;
}
Modified: pkg/ProbABEL/src/main.cpp
===================================================================
--- pkg/ProbABEL/src/main.cpp 2014-05-19 19:27:32 UTC (rev 1734)
+++ pkg/ProbABEL/src/main.cpp 2014-05-19 20:24:52 UTC (rev 1735)
@@ -436,7 +436,7 @@
* equation just below Eq.(4) in the ProbABEL
* paper. TODO LCK
*/
- *chi2[model] << "nan";
+ *chi2[model] << "NaN";
}
else
{
@@ -446,7 +446,7 @@
}
} // END first part of if(poly); allele not too rare
else
- { // SNP is rare: beta, sebeta, chi2 = nan
+ { // SNP is rare: beta, sebeta, chi2 = NaN
int number_of_rows_or_columns = rgd.X.ncol;
start_pos = get_start_position(input_var, model,
number_of_rows_or_columns);
@@ -472,9 +472,9 @@
for (int pos = start_pos; pos <= end_pos; pos++)
{
*beta_sebeta[model] << input_var.getSep()
- << "nan"
+ << "NaN"
<< input_var.getSep()
- << "nan";
+ << "NaN";
}
if (input_var.getNgpreds() == 2)
@@ -486,16 +486,16 @@
{
if (model == 0)
{
- *covvalue[model] << "nan"
+ *covvalue[model] << "NaN"
<< input_var.getSep()
- << "nan";
+ << "NaN";
} else{
- *covvalue[model] << "nan";
+ *covvalue[model] << "NaN";
}
}
#endif
// Oct 26, 2009
- *chi2[model] << "nan";
+ *chi2[model] << "NaN";
} else{
// ngpreds==1 (and SNP is rare)
if (input_var.getInverseFilename() == NULL)
@@ -505,12 +505,12 @@
if (!input_var.getAllcov()
&& input_var.getInteraction() != 0)
{
- *covvalue[model] << "nan";
+ *covvalue[model] << "NaN";
}
#endif
// Oct 26, 2009
} // END if getInverseFilename == NULL
- *chi2[model] << "nan";
+ *chi2[model] << "NaN";
} // END ngpreds == 1 (and SNP is rare)
} // END else: SNP is rare
} // END of model cycle
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