fix typo

sriramlab · Aug 7, 2024 · 1e0f182 · 1e0f182
1 parent 8180cb1
commit 1e0f182
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Showing 13 changed files with 144 additions and 80 deletions.
diff --git a/example/config.txt b/example/config.txt
@@ -3,7 +3,7 @@ phenotype=test.pheno
 covariate=test.cov
 environment=test.env
 annotation=single.annot
-output=test.out
+output=test.mem.out
 nthreads=6
 num_vec=20
 num_jack=10

diff --git a/example/test.2.out b/example/test.2.out
@@ -37,18 +37,18 @@ OUTPUT:
 
 Phenotype 0: 
 Variance components: 
-Sigma^2_g[0] : 0.127387  SE : 0.0236952
-Sigma^2_gxe[0] : 0.241197  SE : 0.123506
-Sigma^2_nxe[0] : 0.155659  SE : 0.12351
-Sigma^2_e : 0.716052  SE : 0.0238489
+Sigma^2_g[0] : 0.136325  SE : 0.0235534
+Sigma^2_gxe[0] : 0.256457  SE : 0.135661
+Sigma^2_nxe[0] : 0.158467  SE : 0.135105
+Sigma^2_e : 0.701567  SE : 0.0237881
 *****
 Heritabilities: 
-h2_g[0] : 0.127211 SE : 0.0236612
-h2_gxe[0] : 0.0957798 SE : 0.0490203
-h2_nxe[0] : 0.0618165 SE : 0.0490491
-Total h2 : 0.284807 SE: 0.0238203
-Total h2_g : 0.127211 SE: 0.0236612
-Total h2_gxe : 0.0957798 SE: 0.0490203
+h2_g[0] : 0.136196 SE : 0.0235355
+h2_gxe[0] : 0.100709 SE : 0.0531341
+h2_nxe[0] : 0.0623701 SE : 0.0531751
+Total h2 : 0.299275 SE: 0.0237595
+Total h2_g : 0.136196 SE: 0.0235355
+Total h2_gxe : 0.100709 SE: 0.0531341
 *****
 Enrichments:
 G enrichment
@@ -57,24 +57,24 @@ Enrichment g[0] : 1 SE : 0
 *****
 Heritabilities and enrichments computed based on overlapping setting
 Heritabilities: 
-h2_g[0] : 0.127211 SE : 0.0236612
+h2_g[0] : 0.136197 SE : 0.0235272
 Enrichments (overlapping def): 
-Enrichment g[0] : 1 SE : 4.03046e-13
+Enrichment g[0] : 1 SE : 0.000212387
 
 Phenotype 1: 
 Variance components: 
-Sigma^2_g[0] : 0.127387  SE : 0.0236952
-Sigma^2_gxe[0] : 0.241197  SE : 0.123506
-Sigma^2_nxe[0] : 0.155659  SE : 0.12351
-Sigma^2_e : 0.716052  SE : 0.0238489
+Sigma^2_g[0] : 0.136325  SE : 0.0235534
+Sigma^2_gxe[0] : 0.256457  SE : 0.135661
+Sigma^2_nxe[0] : 0.158466  SE : 0.135105
+Sigma^2_e : 0.701567  SE : 0.0237881
 *****
 Heritabilities: 
-h2_g[0] : 0.127211 SE : 0.0236612
-h2_gxe[0] : 0.0957798 SE : 0.0490203
-h2_nxe[0] : 0.0618165 SE : 0.0490491
-Total h2 : 0.284807 SE: 0.0238203
-Total h2_g : 0.127211 SE: 0.0236612
-Total h2_gxe : 0.0957798 SE: 0.0490203
+h2_g[0] : 0.136196 SE : 0.0235355
+h2_gxe[0] : 0.100709 SE : 0.0531341
+h2_nxe[0] : 0.0623699 SE : 0.0531751
+Total h2 : 0.299275 SE: 0.0237594
+Total h2_g : 0.136196 SE: 0.0235355
+Total h2_gxe : 0.100709 SE: 0.0531341
 *****
 Enrichments:
 G enrichment
@@ -83,6 +83,6 @@ Enrichment g[0] : 1 SE : 0
 *****
 Heritabilities and enrichments computed based on overlapping setting
 Heritabilities: 
-h2_g[0] : 0.127211 SE : 0.0236612
+h2_g[0] : 0.136197 SE : 0.0235272
 Enrichments (overlapping def): 
-Enrichment g[0] : 1 SE : 3.98454e-13
+Enrichment g[0] : 1.00001 SE : 0.000212251
diff --git a/example/test.mem.out b/example/test.mem.out
@@ -0,0 +1,56 @@
+##################################
+#                                #
+#          GENIE (v1.1.0)        #
+#                                #
+##################################
+
+
+Active essential options: 
+	 - g (genotype) test
+	 - a (annotation) single.annot
+	 - p (phenotype) test.pheno
+	 - c (covariates) test.cov
+	 - o (output) test.mem.out
+	 - e (environment) test.env
+	 - m (model) G
+	 - k (# random vectors) 20
+	 - jn (# jackknife blocks) 10
+	 - t (# threads) 6
+	 - s (seed) 2
+Other options: 
+	 -- norm_proj_pheno (normalize pheno after projection on covariates) 0
+	 -- cov_add_intercept (intercept term added to covariates) 1
+	 - v (verbose) 1
+	 - tr (trace summaries for G only; if pheno is not specified, dummy phenotype is used) 
+
+
+Number of individuals after filtering = 5000
+Number of covariates = 6
+Number of environments = 0
+*****
+Number of SNPs in bin 0 = 10000
+*****
+Number of G variance components = 1
+Number of GxE variance components = 0
+Number of NxE variance components = 0
+*****
+OUTPUT: 
+Variance components: 
+Sigma^2_g[0] : 0.165508  SE : 0.0275589
+Sigma^2_e : 0.834049  SE : 0.0275676
+*****
+Heritabilities: 
+h2_g[0] : 0.165629 SE : 0.0275783
+Total h2 : 0.165629 SE: 0.0275783
+Total h2_g : 0.165629 SE: 0.0275783
+*****
+Enrichments:
+G enrichment
+Enrichment g[0] : 1 SE : 0
+*****
+*****
+Heritabilities and enrichments computed based on overlapping setting
+Heritabilities: 
+h2_g[0] : 0.165645 SE : 0.0275617
+Enrichments (overlapping def): 
+Enrichment g[0] : 1.0001 SE : 0.000198846
diff --git a/example/test.mem.out.MN b/example/test.mem.out.MN
@@ -0,0 +1,2 @@
+NSAMPLE,NSNPS,NBLKS,NBINS,K
+5000,10000,10,1,20
diff --git a/example/test.mem.out.tr b/example/test.mem.out.tr
@@ -0,0 +1,12 @@
+LD_SUM_0,NSNPS_JACKKNIFE
+9141.11,9000
+9103.38,9000
+9072.54,9000
+9038.73,9000
+9152.27,9000
+9214.99,9000
+9102.76,9000
+9221.04,9000
+9150.95,9000
+9101.28,9000
+10160.6,10000
diff --git a/example/test.mem.out.wgxsum b/example/test.mem.out.wgxsum
diff --git a/example/test.mem.out.xsum b/example/test.mem.out.xsum
diff --git a/example/test.out b/example/test.out
@@ -6,71 +6,53 @@
 
 
 Active essential options: 
-	 - g (genotype) inputs/test
-	 - annot (annotation) inputs/multi.1.annot
-	 - p (phenotype) inputs/test.pheno
-	 - c (covariates) inputs/test.cov
-	 - o (output) test.out
-	 - e (environment) inputs/test.env
-	 - m (model) G
-	 - k (# random vectors) 20
-	 - jn (# jackknife blocks) 10
-	 - t (# threads) 1
-	 - s (seed) 1
-Other options: 
-	 - norm_proj_pheno (normalize pheno after projection on covariates) 0
-	 - cov_add_intercept (intercept term added to covariates) 1
-	 - v (verbose) 3
-	 - tr (trace summaries) 
-
-
-Number of individuals after filtering = 5000
-Number of covariates = 6
-Number of environments = 0
-Jackknife block = 0
-Xl[0] = 8524.55 5025.76 4995.18
-5025.76 17628.4 4994.74
-4995.18 4994.74    4994
-Yr[0] = 5428.16
-5404.06
-4992.07
-Normal Equations info:
-The relative error is: 7.55282e-08
-Max sing.val: 22410.2
-Min sing.val: 1343.42
-Condition number: 16.6815
+	-g (genotype) test
+	-a (annotation) single.annot
+	-p (phenotype) test.pheno
+	-c (covariates) test.cov
+	-o (output) test.out
+	-e (environment) test.env
+	-m (model) G+GxE+NxE
+	-k (# random vectors) 10
+	-jn (# jackknife blocks) 10
+	-t (# threads) 6
+	-s (seed) 1
 
 
+Number of individuals after filtering: 5000
+Number of covariates: 7
+Number of environments: 1
 *****
-Number of SNPs in bin 0 = 8015
-Number of SNPs in bin 1 = 1985
+Number of features in bin 0 : 10000
+Number of features in bin 1 : 10000
+Number of features in bin 2 : 1
 *****
-Number of G variance components = 2
-Number of GxE variance components = 0
-Number of NxE variance components = 0
+Number of G variance components : 1
+Number of GxE variance components : 1
+Number of NxE variance components : 1
 *****
 OUTPUT: 
 Variance components: 
-Sigma^2_g[0] : 0.136719  SE : 0.0362664
-Sigma^2_g[1] : 0.0323202  SE : 0.0194803
-Sigma^2_e : 0.830534  SE : 0.0296515
+Sigma^2_g[0] : 0.12992  SE : 0.0256735
+Sigma^2_gxe[0] : 0.250272  SE : 0.117951
+Sigma^2_nxe[0] : 0.166822  SE : 0.117721
+Sigma^2_e : 0.707313  SE : 0.0258222
 *****
 Heritabilities: 
-h2_g[0] : 0.136807 SE : 0.0362822
-h2_g[1] : 0.0323374 SE : 0.0194907
-Total h2 : 0.169144 SE: 0.029663
-Total h2_g : 0.169144 SE: 0.029663
+h2_g[0] : 0.12979 SE : 0.0256438
+h2_gxe[0] : 0.0982365 SE : 0.0463089
+h2_nxe[0] : 0.0655094 SE : 0.0462279
+Total h2 : 0.293536 SE: 0.0257912
+Total h2_g : 0.12979 SE: 0.0256438
+Total h2_gxe : 0.0982365 SE: 0.0463088
 *****
 Enrichments:
 G enrichment
-Enrichment g[0] : 1.00913 SE : 0.0544947
-Enrichment g[1] : 0.963136 SE : 0.215183
+Enrichment g[0] : 1 SE : 0
 *****
 *****
 Heritabilities and enrichments computed based on overlapping setting
 Heritabilities: 
-h2_g[0] : 0.136805 SE : 0.0362711
-h2_g[1] : 0.0323371 SE : 0.0194909
+h2_g[0] : 0.129789 SE : 0.0256496
 Enrichments (overlapping def): 
-Enrichment g[0] : 1.00911 SE : 0.0544469
-Enrichment g[1] : 0.963125 SE : 0.2152
+Enrichment g[0] : 0.999993 SE : 0.000172287
diff --git a/example/test.out.MN b/example/test.out.MN
@@ -1,2 +1,2 @@
-NSAMPLE,NSNP,NBLK,NBIN
-5000,10000,10,2
+NSAMPLE,NSNPS,NBLKS,NBINS,K
+5000,10000,10,1,20
diff --git a/example/test.out.tr b/example/test.out.tr
@@ -0,0 +1,12 @@
+LD_SUM_0,NSNPS_JACKKNIFE
+9141.11,9000
+9103.38,9000
+9072.54,9000
+9038.73,9000
+9152.27,9000
+9214.99,9000
+9102.76,9000
+9221.04,9000
+9150.95,9000
+9101.28,9000
+10160.6,10000
diff --git a/example/test.out.wgxsum b/example/test.out.wgxsum
diff --git a/example/test.out.xsum b/example/test.out.xsum
diff --git a/example/test.sh b/example/test.sh
@@ -4,6 +4,6 @@ covar=test.cov
 annot=single.annot
 env=test.env
 
-../build/GENIE -g $gen -p $phen -c $covar -e $env -m G+GxE+NxE  -k 10 -jn 10  -o test.out -annot $annot -t 6 -s 1
-# ../build/GENIE_multi_pheno -g $gen -p ./test.2.pheno -c $covar -e $env -m G+GxE+NxE  -k 10 -jn 10  -o test.2.out -annot $annot -t 6
+../build/GENIE -g $gen -p $phen -c $covar -e $env -m G+GxE+NxE  -k 10 -jn 10  -o test.out --annot $annot -t 6 -s 1
+# ../build/GENIE_multi_pheno -g $gen -p ./test.2.pheno -c $covar -e $env -m G+GxE+NxE  -k 10 -jn 10  -o test.2.out --annot $annot -t 6
 # ../build/GENIE_mem --config ./config.txt
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		NSAMPLE,NSNPS,NBLKS,NBINS,K
		5000,10000,10,1,20