[Genabel-commits] r1212 - in pkg/ProbABEL: examples tests/verified_results

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-05-13 09:41:14 +0200 (Mon, 13 May 2013)
New Revision: 1212

Modified:
   pkg/ProbABEL/examples/test.mlinfo
   pkg/ProbABEL/tests/verified_results/height_add.out.txt
   pkg/ProbABEL/tests/verified_results/height_base_add.out.txt
Log:
Added multi-allelic A1 and A2 to mlinfo file. This is to check whether bug #2586 reappears again. 



Modified: pkg/ProbABEL/examples/test.mlinfo
===================================================================
--- pkg/ProbABEL/examples/test.mlinfo	2013-05-10 21:38:05 UTC (rev 1211)
+++ pkg/ProbABEL/examples/test.mlinfo	2013-05-13 07:41:14 UTC (rev 1212)
@@ -1,6 +1,6 @@
 SNP	Al1	Al2	Freq1	MAF	Quality	Rsq
-rs7247199	G	A	0.5847	0.4150	0.9299	0.8666
-rs8102643	C	T	0.5847	0.4150	0.9308	0.8685
+rs7247199	GAC	A	0.5847	0.4150	0.9299	0.8666
+rs8102643	C	TGGT	0.5847	0.4150	0.9308	0.8685
 rs8102615	T	A	0.5006	0.4702	0.9375	0.8932
 rs8105536	G	A	0.5783	0.4213	0.9353	0.8832
 rs2312724	T	C	0.9122	0.0877	0.9841	0.9232

Modified: pkg/ProbABEL/tests/verified_results/height_add.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_add.out.txt	2013-05-10 21:38:05 UTC (rev 1211)
+++ pkg/ProbABEL/tests/verified_results/height_add.out.txt	2013-05-13 07:41:14 UTC (rev 1212)
@@ -1,6 +1,6 @@
 name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_add sebeta_SNP_add loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 20.3847112 76.6301612 -428.98
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -25.763226 86.4877202 -426.965
-rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -40.7722369 102.559115 -428.936
-rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 35.3601998 81.7868565 -428.921
-rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 -112.234833 141.168963 -428.694
+rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 19 204938 20.3847112 76.6301612 -428.98
+rs8102643 C TGGT 0.5847 0.415 0.9308 0.8685 181 0.808177 19 207859 -25.763226 86.4877202 -426.965
+rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 19 211970 -40.7722369 102.559115 -428.936
+rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 19 212033 35.3601998 81.7868565 -428.921
+rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 19 217034 -112.234833 141.168963 -428.694

Modified: pkg/ProbABEL/tests/verified_results/height_base_add.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_base_add.out.txt	2013-05-10 21:38:05 UTC (rev 1211)
+++ pkg/ProbABEL/tests/verified_results/height_base_add.out.txt	2013-05-13 07:41:14 UTC (rev 1212)
@@ -1,6 +1,6 @@
 name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_add sebeta_SNP_add loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 19 204938 20.3847112 76.6301612 -428.98
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 19 207859 -25.763226 86.4877202 -426.965
+rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 19 204938 20.3847112 76.6301612 -428.98
+rs8102643 C TGGT 0.5847 0.415 0.9308 0.8685 181 0.808177 19 207859 -25.763226 86.4877202 -426.965
 rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 19 211970 -40.7722369 102.559115 -428.936
 rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 19 212033 35.3601998 81.7868565 -428.921
 rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 19 217034 -112.234833 141.168963 -428.694