[Genabel-commits] r1287 - in pkg/ProbABEL/tests: . test_cox_ngpreds2 verified_results
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Aug 8 13:23:25 CEST 2013
Author: lckarssen
Date: 2013-08-08 13:23:24 +0200 (Thu, 08 Aug 2013)
New Revision: 1287
Modified:
pkg/ProbABEL/tests/Makefile.am
pkg/ProbABEL/tests/test_cox_ngpreds2/run_models_in_R_palinear.R
pkg/ProbABEL/tests/verified_results/height_add.out.txt
pkg/ProbABEL/tests/verified_results/height_base_add.out.txt
pkg/ProbABEL/tests/verified_results/height_ngp2_2df.out.txt
pkg/ProbABEL/tests/verified_results/height_ngp2_add.out.txt
pkg/ProbABEL/tests/verified_results/height_ngp2_domin.out.txt
pkg/ProbABEL/tests/verified_results/height_ngp2_over_domin.out.txt
pkg/ProbABEL/tests/verified_results/height_ngp2_recess.out.txt
Log:
Updated the ProbABEL tests to reflect the changes in the previous
commit where chi^2 values were added to the output of palinear.
Extended tests/test_cox_ngpreds2/run_models_in_R_palinear.R (actually
that directory should be renamed now...) so that the ProbABEL output
is now compared to the R output and errors are printed when there is a
descrepancy. I've set the tolerance for the checks to 1e-5.
Copyright of this change lies with the Erasmus MC.
Modified: pkg/ProbABEL/tests/Makefile.am
===================================================================
--- pkg/ProbABEL/tests/Makefile.am 2013-08-08 11:19:30 UTC (rev 1286)
+++ pkg/ProbABEL/tests/Makefile.am 2013-08-08 11:23:24 UTC (rev 1287)
@@ -2,8 +2,8 @@
AUTOMAKE_OPTIONS = foreign color-tests
-#tests_files = check_probabel.pl_chunk.sh check_dose_input.sh
-tests_files = check_dose_input.sh
+tests_files = check_probabel.pl_chunk.sh check_dose_input.sh
+
verified_results = verified_results/height_add.out.txt \
verified_results/height_ngp2_add.out.txt \
verified_results/height_ngp2_2df.out.txt \
Modified: pkg/ProbABEL/tests/test_cox_ngpreds2/run_models_in_R_palinear.R
===================================================================
--- pkg/ProbABEL/tests/test_cox_ngpreds2/run_models_in_R_palinear.R 2013-08-08 11:19:30 UTC (rev 1286)
+++ pkg/ProbABEL/tests/test_cox_ngpreds2/run_models_in_R_palinear.R 2013-08-08 11:23:24 UTC (rev 1287)
@@ -1,74 +1,241 @@
-###
-# load the data
-###
+## Set tolerance for comparing various outputs
+tol <- 1e-5
-# load phenotypic data
+####
+## load the data
+####
+
+## load phenotypic data
pheno <- read.table("../../examples/height.txt", head=TRUE, string=FALSE)
-# load genetic DOSE data
+## load genetic DOSE data
dose <- read.table("../../examples/test.mldose", head=FALSE, string=FALSE)
-# remove "1->" from the names of dose-IDs
+## remove "1->" from the names of dose-IDs
idNames <- dose[, 1]
idNames <- sub("[0-9]+->", "", idNames)
dose[, 1] <- idNames
-# check consistency of names
-table(dose[, 1] == pheno[, 1])
+cat("Dose: check consistency of names\t\t")
+stopifnot( all.equal(dose[, 1], pheno[, 1], tol) )
+cat("OK\n")
-# load genetic PROB data
+## load genetic PROB data
prob <- read.table("../../examples/test.mlprob", head=FALSE, string=FALSE)
-# remove "1->" from the names of prob-IDs
+## remove "1->" from the names of prob-IDs
idNames <- prob[, 1]
idNames <- sub("[0-9]+->", "", idNames)
prob[, 1] <- idNames
-# check consistency of names
-table(prob[, 1] == pheno[, 1])
+cat("Prob: check consistency of names\t\t")
+stopifnot( all.equal(prob[, 1], pheno[, 1], tol) )
+cat("OK\n")
-# check consistency DOSE <-> PROB
+## check consistency DOSE <-> PROB
doseFromProb <- matrix(NA, ncol=dim(dose)[2], nrow=dim(dose)[1])
for (i in 3:dim(dose)[2]) {
indexHom <- 3 + ( i - 3 ) * 2
indexHet <- indexHom + 1
doseFromProb[, i] <- prob[, indexHom] * 2 + prob[, indexHet]
- print( table( ( dose[, i] - doseFromProb[, i] ) > 1e-8 ) )
}
+cat("Check consistency dose <-> prob\t\t\t")
+stopifnot( all.equal(dose[, 3:ncol(dose)],
+ as.data.frame(doseFromProb)[,3:ncol(doseFromProb)],
+ tol=tol )
+ )
+cat("OK\n")
-###
-# run analysis
-###
+####
+## Run ProbABEL to get the output data we want to compare/verify
+####
+cat("Running ProbABEL...\t\t\t\t")
+tmp <- system("cd ../../examples/; sh example_qt.sh; cd -",
+ intern=TRUE)
+cat("OK\n")
+resPaAddDose <-
+ read.table("../../examples/height_base_add.out.txt",
+ head=TRUE)[,
+ c("beta_SNP_add",
+ "sebeta_SNP_add",
+ "chi2_SNP")]
+resPaAddProb <-
+ read.table("../../examples/height_ngp2_add.out.txt",
+ head=TRUE)[,
+ c("beta_SNP_addA1",
+ "sebeta_SNP_addA1",
+ "chi2_SNP_A1")]
+resPaDom <-
+ read.table("../../examples/height_ngp2_domin.out.txt",
+ head=TRUE)[,
+ c("beta_SNP_domA1",
+ "sebeta_SNP_domA1",
+ "chi2_SNP_domA1")]
+resPaRec <-
+ read.table("../../examples/height_ngp2_recess.out.txt",
+ head=TRUE)[,
+ c("beta_SNP_recA1",
+ "sebeta_SNP_recA1",
+ "chi2_SNP_recA1")]
+resPaOdom <-
+ read.table("../../examples/height_ngp2_over_domin.out.txt",
+ head=TRUE)[,
+ c("beta_SNP_odomA1",
+ "sebeta_SNP_odomA1",
+ "chi2_SNP_odomA1")]
+resPa2df <-
+ read.table("../../examples/height_ngp2_2df.out.txt",
+ head=TRUE)[,
+ c("beta_SNP_A1A2",
+ "sebeta_SNP_A1A2",
+ "beta_SNP_A1A1",
+ "sebeta_SNP_A1A1",
+ "chi2_SNP_2df")]
+
+####
+## run analysis in R
+####
attach(pheno)
-# run analysis on dose
+cat("Comparing R output with ProbABEL output\t\t")
+## run analysis on dose
+dose.add.R <- data.frame(beta_SNP_add = numeric(),
+ sebeta_SNP_add = numeric(),
+ chi2_SNP = numeric())
+prob.add.R <- data.frame(beta_SNP_addA1 = numeric(),
+ sebeta_SNP_addA1 = numeric(),
+ chi2_SNP_A1 = numeric())
for (i in 3:dim(dose)[2]) {
- smr <- summary( lm( height ~ sex + age + dose[, i] ) )
- print( smr$coef[4, 1:2] )
- smr <- summary( lm( height ~ sex + age + doseFromProb[, i] ) )
- print( smr$coef[4, 1:2] )
+ noNA <- which( !is.na(dose[, i]) )
+ model.0 <- lm( height[noNA] ~ sex[noNA] + age[noNA] )
+
+ model.dose <- lm( height ~ sex + age + dose[, i] )
+ sm.dose <- summary(model.dose)$coef[4, 1:2]
+
+ model.prob <- lm( height ~ sex + age + doseFromProb[, i] )
+ sm.prob <- summary(model.prob)$coef[4, 1:2]
+
+ lrt.dose <- 2 * ( logLik( model.dose ) - logLik( model.0 ) )
+ lrt.prob <- 2 * ( logLik( model.prob ) - logLik( model.0 ) )
+
+ row <- data.frame(
+ beta_SNP_add = sm.dose[1],
+ sebeta_SNP_add = sm.dose[2],
+ chi2_SNP = lrt.dose)
+ dose.add.R <- rbind(dose.add.R, row)
+
+ row <- data.frame(
+ beta_SNP_addA1 = sm.prob[1],
+ sebeta_SNP_addA1 = sm.prob[2],
+ chi2_SNP_A1 = lrt.prob)
+ prob.add.R <- rbind(prob.add.R, row)
}
+rownames(dose.add.R) <- NULL
+rownames(prob.add.R) <- NULL
+stopifnot( all.equal(resPaAddDose, dose.add.R, tol=tol) )
-# dominant model
+stopifnot( all.equal(resPaAddProb, prob.add.R, tol=tol) )
+
+
+## dominant model
+prob.dom.R <- data.frame(beta_SNP_domA1 = numeric(),
+ sebeta_SNP_domA1 = numeric(),
+ chi2_SNP_domA1 = numeric())
for (i in 3:dim(dose)[2]) {
indexHom <- 3 + ( i - 3 ) * 2
indexHet <- indexHom + 1
- regProb <- prob[, indexHom] + prob[, indexHet]
- smr <- summary( lm( height ~ sex + age + regProb ) )
- print( smr$coef[4, 1:2] )
+ regProb <- prob[, indexHom] + prob[, indexHet]
+
+ noNA <- which( !is.na(regProb) )
+ model.0 <- lm( height[noNA] ~ sex[noNA] + age[noNA] )
+ model <- lm( height ~ sex + age + regProb )
+ sm <- summary(model)$coef[4, 1:2]
+ lrt <- 2 * ( logLik( model ) - logLik( model.0 ) )
+
+ row <- data.frame(
+ beta_SNP_domA1 = sm[1],
+ sebeta_SNP_domA1 = sm[2],
+ chi2_SNP_domA1 = lrt)
+ prob.dom.R <- rbind(prob.dom.R, row)
}
+rownames(prob.dom.R) <- NULL
+stopifnot( all.equal(resPaDom, prob.dom.R, tol=tol) )
-# recessive model
+
+## recessive model
+prob.rec.R <- data.frame(beta_SNP_recA1 = numeric(),
+ sebeta_SNP_recA1 = numeric(),
+ chi2_SNP_recA1 = numeric())
for (i in 3:dim(dose)[2]) {
indexHom <- 3 + ( i - 3 ) * 2
indexHet <- indexHom + 1
regProb <- prob[, indexHom]
- smr <- summary( lm( height ~ sex + age + regProb ) )
- print( smr$coef[4, 1:2] )
+
+ noNA <- which( !is.na(regProb) )
+ model.0 <- lm( height[noNA] ~ sex[noNA] + age[noNA] )
+ model <- lm( height ~ sex + age + regProb )
+ sm <- summary(model)$coef[4, 1:2]
+ lrt <- 2 * ( logLik( model ) - logLik( model.0 ) )
+
+ row <- data.frame(
+ beta_SNP_recA1 = sm[1],
+ sebeta_SNP_recA1 = sm[2],
+ chi2_SNP_recA1 = lrt)
+ prob.rec.R <- rbind(prob.rec.R, row)
}
+rownames(prob.rec.R) <- NULL
+stopifnot( all.equal(resPaRec, prob.rec.R, tol=tol) )
-# over-dominant model
+
+## over-dominant model
+prob.odom.R <- data.frame(beta_SNP_odomA1 = numeric(),
+ sebeta_SNP_odomA1 = numeric(),
+ chi2_SNP_odomA1 = numeric())
for (i in 3:dim(dose)[2]) {
indexHom <- 3 + ( i - 3 ) * 2
indexHet <- indexHom + 1
regProb <- prob[, indexHet]
- smr <- summary( lm( height ~ sex + age + regProb ) )
- print( smr$coef[4, 1:2] )
+
+ noNA <- which( !is.na(regProb) )
+ model.0 <- lm( height[noNA] ~ sex[noNA] + age[noNA] )
+ model <- lm( height ~ sex + age + regProb )
+ sm <- summary(model)$coef[4, 1:2]
+ lrt <- 2 * ( logLik( model ) - logLik( model.0 ) )
+
+ row <- data.frame(
+ beta_SNP_odomA1 = sm[1],
+ sebeta_SNP_odomA1 = sm[2],
+ chi2_SNP_odomA1 = lrt)
+ prob.odom.R <- rbind(prob.odom.R, row)
}
+rownames(prob.odom.R) <- NULL
+stopifnot( all.equal(resPaOdom, prob.odom.R, tol=tol) )
+
+
+## 2df model
+prob.2df.R <- data.frame(beta_SNP_A1A2 = numeric(),
+ sebeta_SNP_A1A2 = numeric(),
+ beta_SNP_A1A1 = numeric(),
+ sebeta_SNP_A1A1 = numeric(),
+ chi2_SNP_2df = numeric())
+for (i in 3:dim(dose)[2]) {
+ indexHom <- 3 + ( i - 3 ) * 2
+ indexHet <- indexHom + 1
+ regProb <- prob[, indexHet]
+
+ noNA <- which( !is.na(regProb) )
+ model.0 <- lm( height[noNA] ~ sex[noNA] + age[noNA] )
+ model <- lm( height ~ sex + age + prob[, indexHet] + prob[, indexHom] )
+ smA1A2 <- summary(model)$coef[4, 1:2]
+ smA1A1 <- summary(model)$coef[5, 1:2]
+ lrt <- 2 * ( logLik( model ) - logLik( model.0 ) )
+
+ row <- data.frame(
+ beta_SNP_A1A2 = smA1A2[1],
+ sebeta_SNP_A1A2 = smA1A2[2],
+ beta_SNP_A1A1 = smA1A1[1],
+ sebeta_SNP_A1A1 = smA1A1[2],
+ chi2_SNP_2df = lrt)
+ prob.2df.R <- rbind(prob.2df.R, row)
+}
+rownames(prob.2df.R) <- NULL
+stopifnot( all.equal(resPa2df, prob.2df.R, tol=tol) )
+
+cat("OK\n")
Modified: pkg/ProbABEL/tests/verified_results/height_add.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_add.out.txt 2013-08-08 11:19:30 UTC (rev 1286)
+++ pkg/ProbABEL/tests/verified_results/height_add.out.txt 2013-08-08 11:23:24 UTC (rev 1287)
@@ -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 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 20.3847112 76.6301612 -428.98
-rs8102643 C TGGT 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
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_add sebeta_SNP_add chi2_SNP
+rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 20.3847 76.6302 0.0723394
+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 0.9232 182 0.933464 2 217034 -112.235 141.169 0.645146
Modified: pkg/ProbABEL/tests/verified_results/height_base_add.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_base_add.out.txt 2013-08-08 11:19:30 UTC (rev 1286)
+++ pkg/ProbABEL/tests/verified_results/height_base_add.out.txt 2013-08-08 11:23:24 UTC (rev 1287)
@@ -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 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
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_add sebeta_SNP_add chi2_SNP
+rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 19 204938 20.3847 76.6302 0.0723394
+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 0.9232 182 0.933464 19 217034 -112.235 141.169 0.645146
Modified: pkg/ProbABEL/tests/verified_results/height_ngp2_2df.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_2df.out.txt 2013-08-08 11:19:30 UTC (rev 1286)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_2df.out.txt 2013-08-08 11:23:24 UTC (rev 1287)
@@ -1,6 +1,6 @@
-name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_A1A2 beta_SNP_A1A1 sebeta_SNP_A1A2 sebeta_SNP_A1A1 loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 615.049 1057.49 -539.487 1040.54 -428.817
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -820.352 1392.51 -646.025 1054.18 -426.797
-rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -239.797 1308.51 -246.735 1102.06 -428.924
-rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 782.576 1474.59 604.391 1064.24 -428.789
-rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 1180.53 1104.39 912.574 1003.85 -427.981
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_A1A2 sebeta_SNP_A1A2 beta_SNP_A1A1 sebeta_SNP_A1A1 chi2_SNP_2df
+rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 615.017 1057.49 -539.456 1040.54 0.398888
+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 0.9232 182 0.933464 2 217034 1180.51 1104.39 912.561 1003.84 2.07178
Modified: pkg/ProbABEL/tests/verified_results/height_ngp2_add.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_add.out.txt 2013-08-08 11:19:30 UTC (rev 1286)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_add.out.txt 2013-08-08 11:23:24 UTC (rev 1287)
@@ -1,6 +1,6 @@
-name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_addA1 sebeta_SNP_addA1 loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 20.3848 76.6301 -428.98
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -25.7626 86.4878 -426.965
-rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -40.7723 102.559 -428.936
-rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 35.361 81.7867 -428.921
-rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 -112.234 141.168 -428.694
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_addA1 sebeta_SNP_addA1 chi2_SNP_A1
+rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 20.3847 76.6302 0.0723394
+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 0.9232 182 0.933464 2 217034 -112.235 141.169 0.645146
Modified: pkg/ProbABEL/tests/verified_results/height_ngp2_domin.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_domin.out.txt 2013-08-08 11:19:30 UTC (rev 1286)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_domin.out.txt 2013-08-08 11:23:24 UTC (rev 1287)
@@ -1,6 +1,6 @@
-name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_domA1 sebeta_SNP_domA1 loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 33.0595 115.333 -428.974
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -178.128 417.233 -426.917
-rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -272.156 640.297 -428.924
-rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 188.396 361.092 -428.877
-rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 285.007 898.508 -428.965
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_domA1 sebeta_SNP_domA1 chi2_SNP_domA1
+rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 33.0592 115.333 0.0839902
+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 0.9232 182 0.933464 2 217034 285.012 898.512 0.10285
Modified: pkg/ProbABEL/tests/verified_results/height_ngp2_over_domin.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_over_domin.out.txt 2013-08-08 11:19:30 UTC (rev 1286)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_over_domin.out.txt 2013-08-08 11:23:24 UTC (rev 1287)
@@ -1,6 +1,6 @@
-name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_odom sebeta_SNP_odom loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 80.0816 231.105 -428.955
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 28.4979 142.757 -426.989
-rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 51.4168 142.042 -428.95
-rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 -50.7539 145.509 -428.954
-rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 188.854 172.317 -428.404
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_odomA1 sebeta_SNP_odomA1 chi2_SNP_odomA1
+rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 80.0802 231.105 0.122726
+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 0.9232 182 0.933464 2 217034 188.854 172.317 1.22402
Modified: pkg/ProbABEL/tests/verified_results/height_ngp2_recess.out.txt
===================================================================
--- pkg/ProbABEL/tests/verified_results/height_ngp2_recess.out.txt 2013-08-08 11:19:30 UTC (rev 1286)
+++ pkg/ProbABEL/tests/verified_results/height_ngp2_recess.out.txt 2013-08-08 11:23:24 UTC (rev 1287)
@@ -1,6 +1,6 @@
-name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_recA1 sebeta_SNP_recA1 loglik
-rs7247199 G A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 51.0128 227.445 -428.991
-rs8102643 C T 0.5847 0.415 0.9308 0.8685 181 0.808177 1 207859 -28.2735 108.063 -426.975
-rs8102615 T A 0.5006 0.4702 0.9375 0.8932 182 0.8665 2 211970 -45.9706 119.627 -428.941
-rs8105536 G A 0.5783 0.4213 0.9353 0.8832 182 0.791701 2 212033 42.3583 105.005 -428.933
-rs2312724 T C 0.9122 0.0877 0.9841 0.9232 182 0.933464 2 217034 -147.318 156.768 -428.566
+name A1 A2 Freq1 MAF Quality Rsq n Mean_predictor_allele chrom position beta_SNP_recA1 sebeta_SNP_recA1 chi2_SNP_recA1
+rs7247199 GAC A 0.5847 0.415 0.9299 0.8666 182 0.333668 1 204938 51.0131 227.445 0.051428
+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 0.9232 182 0.933464 2 217034 -147.318 156.768 0.900685
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