[Genabel-commits] r715 - in pkg/ProbABEL: . doc src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun May 15 22:47:37 CEST 2011
Author: lckarssen
Date: 2011-05-15 22:47:37 +0200 (Sun, 15 May 2011)
New Revision: 715
Modified:
pkg/ProbABEL/Makefile
pkg/ProbABEL/doc/CHANGES.LOG
pkg/ProbABEL/src/version.h
Log:
Updated version number for ProbABEL to 0.1-9e for upcoming release of tar-ball.
Modified: pkg/ProbABEL/Makefile
===================================================================
--- pkg/ProbABEL/Makefile 2011-05-15 20:32:03 UTC (rev 714)
+++ pkg/ProbABEL/Makefile 2011-05-15 20:47:37 UTC (rev 715)
@@ -1,4 +1,4 @@
-VERSION = 0.1-9d
+VERSION = 0.1-9e
SRCDIR = src
BINDIR = bin
DOCDIR = doc
@@ -45,4 +45,4 @@
distrib: linux_distrib clean win_distrib clean
-.PHONY: distrib linux_distrib win_distrib clean clean_doc
\ No newline at end of file
+.PHONY: distrib linux_distrib win_distrib clean clean_doc
Modified: pkg/ProbABEL/doc/CHANGES.LOG
===================================================================
--- pkg/ProbABEL/doc/CHANGES.LOG 2011-05-15 20:32:03 UTC (rev 714)
+++ pkg/ProbABEL/doc/CHANGES.LOG 2011-05-15 20:47:37 UTC (rev 715)
@@ -1,3 +1,8 @@
+***** v.0.1-9e (2011.05.15)
+Previous version wouldn't compile because of missing frerror. file.
+Fixes bug #1339 (the bug fix was done a month ago, but no package had
+been release since then).
+
***** v.0.1-9d (2010.10.08)
fix related to compilation with updated 'filevector' library
@@ -13,7 +18,7 @@
correct subject IDs. We were able to overcome the problems in the data
after the fix and submit analysis successfully.
-Bravo, Vadim! Thumbs up, and many thanks from us (and of cause all users)!
+Bravo, Vadim! Thumbs up, and many thanks from us (and of course all users)!
***** v.0.1-9b (2010.06.02)
@@ -32,7 +37,7 @@
***** v.0.1-6b (2010.04.22)
-error message with missing map-file reported absence of
+error message with missing map-file reported absence of
other file, fixed: thanks to N. Pirastu for noticing!
***** v.0.1-6 (2010.04.02)
@@ -49,10 +54,10 @@
***** v.0.1-4 (2010.02.12)
-Instead chi2, log-likelihood is reported
+Instead chi2, log-likelihood is reported
ProbABEL can now work in very low memory mode, using filevector library
-(see examples/prepare_data.R for examples how to convert data from
+(see examples/prepare_data.R for examples how to convert data from
MACH to filevector format).
Can also treat missing values (NA, nan)
@@ -60,52 +65,52 @@
***** v.0.1-3 (2009.11.25)
This version is courtesy of Han Chen (Nov 9, 2009). The modifications allow
-to extract the covariance between the estimate of beta(SNP) and the estimate
-of beta(interaction). This information can be used to, e.g., to perform a
+to extract the covariance between the estimate of beta(SNP) and the estimate
+of beta(interaction). This information can be used to, e.g., to perform a
rigorous 2df meta-analysis of interactions later on.
Here is a more detailed description of what the changes concern (by Han Chen):
-For model
+For model
Y = b_0 + b_cov1 * cov1 + b_cov2 * cov2 + ... + b_covN * covN + b_SNP * SNP + b_covX_SNP * covX * SNP
-(1<=X<=N, covX can be any covariate in the phenotype file, from cov1 to covN,
-option --interaction=X, see ProbABEL manual for details)
-Or model
+(1<=X<=N, covX can be any covariate in the phenotype file, from cov1 to covN,
+option --interaction=X, see ProbABEL manual for details)
+Or model
Y = b_0 + b_cov1 * cov1 + b_cov2 * cov2 + ... + b_covX-1 * covX-1 + b_covX+1 * covX+1 + ... + b_covN * covN + b_SNP * SNP + b_covX_SNP * covX * SNP
-(1<=X<=N, covX can be any covariate in the phenotype file, from cov1 to covN,
+(1<=X<=N, covX can be any covariate in the phenotype file, from cov1 to covN,
option --interaction_only=X, see ProbABEL manual for details)
-This "plus" version reports naive covariance (default) or robust covariance
-(option --robust) between b_SNP and b_covX_SNP estimates, for palinear and
+This "plus" version reports naive covariance (default) or robust covariance
+(option --robust) between b_SNP and b_covX_SNP estimates, for palinear and
palogist (can NOT report covariance for pacoxph, Cox regression).
Covariances are no reported for options --score, --allcov, --mmscore
-LINEAR REGRESSION OR LOGISTIC REGRESSION ONLY
+LINEAR REGRESSION OR LOGISTIC REGRESSION ONLY
-Bravo, Han! -- and many thanks!
+Bravo, Han! -- and many thanks!
***** v.0.1-2 (2009.10.19)
-Minor bug fix: allele frequency was estimated wrongly when option --ngpreds=2
+Minor bug fix: allele frequency was estimated wrongly when option --ngpreds=2
was used. The bug had no effect anything else (betas, ses, chi2s were correct).
-Many thanks to Han Chen (Boston University) for identification of this bug
+Many thanks to Han Chen (Boston University) for identification of this bug
and providing us with an excellent summary which allowed fixing the bug easily!
***** v.0.1-1 (2009.09.22)
Added "robust" option, which computes SEs using formula
(X'X)^(-1) (X' V X) (X'X)^(-1) where V is diagonal matrix containing
-squares of residuals. In standard analysis, V is diagonal matrix
+squares of residuals. In standard analysis, V is diagonal matrix
containing constant = RSS/N
***** v.0.1-0 (2009.08.15)
-fixed a bug in phedata class: if ID was starting with 'N' or 'n', it
-was counted as NA (thanks to Youfan & Ida Surakka for pointing the
+fixed a bug in phedata class: if ID was starting with 'N' or 'n', it
+was counted as NA (thanks to Youfan & Ida Surakka for pointing the
bug out)
@@ -125,7 +130,7 @@
***** v.0.0-7 (2009.03.19)
-Bug with interaction in survival analysis fixed.
+Bug with interaction in survival analysis fixed.
***** v.0.0-6 (2009.01.28)
@@ -142,20 +147,20 @@
***** v.0.0-5d (2009.01.11)
-Possibility of analysis for SNP interaction has been added.
+Possibility of analysis for SNP interaction has been added.
New key is --interaction=<covariate number>.
Default is --interaction=0. The first covariate is --interaction=1.
Output organizing has been changed. Now there is one file per one model.
-Output file names consist of prefix which goes together with input
+Output file names consist of prefix which goes together with input
parameter --out and one of following postfixes:
"_2df.out.txt", "_add.out.txt", "_domin.out.txt", "_recess.out.txt", "_over_domin.out.txt".
If postfix is not given name "regression" is used.
-File bin/probabel_system_example.pl has been changedand renamed
-to probabel.pl_example. This script combines all ProbABEL functions and allows
-you to organize work with your MACH output files. Just change configuration
+File bin/probabel_system_example.pl has been changedand renamed
+to probabel.pl_example. This script combines all ProbABEL functions and allows
+you to organize work with your MACH output files. Just change configuration
file probabel_config.cfg_example and probabel.pl_example like it is written in manual.
Now chi2 is likelihood ration test when null model is without SNP and alternative - with SNP and interaction.
@@ -163,13 +168,13 @@
***** v.0.0-5c (2008.12.05)
-Changed presentation of output: effective allele (A1) is mentioned
+Changed presentation of output: effective allele (A1) is mentioned
in exact manner
***** v.0.0-5b (2008.11.20)
-Output from analysis with ngpred=2 (MLPROB files) fixed (models were
+Output from analysis with ngpred=2 (MLPROB files) fixed (models were
named wrongly)
@@ -177,19 +182,19 @@
--allcov option added (allows output of estimates for all covariates)
-example system-wide perl script running the analysis for
-(potentially multiple cohorts) and joining single-chomosome
+example system-wide perl script running the analysis for
+(potentially multiple cohorts) and joining single-chomosome
outputs to single file provided
-A change in the procedure to read genotypic files, read format of the
-beging of every line changed from "%d->%s" to "%[^->]->%[^->]" (thanks to
+A change in the procedure to read genotypic files, read format of the
+beging of every line changed from "%d->%s" to "%[^->]->%[^->]" (thanks to
Bertram Muller-Myhsok & Benno Puetz)
***** v.0.0-5 (2008.06.07)
-More than one genomic predictor per point: possibility to
-work with MLPROB files (options --ngpreds added).
+More than one genomic predictor per point: possibility to
+work with MLPROB files (options --ngpreds added).
***** v.0.0-4 (2008.05.20)
@@ -208,4 +213,3 @@
Output generated in tab-delimited format
Documentation updated
-
Modified: pkg/ProbABEL/src/version.h
===================================================================
--- pkg/ProbABEL/src/version.h 2011-05-15 20:32:03 UTC (rev 714)
+++ pkg/ProbABEL/src/version.h 2011-05-15 20:47:37 UTC (rev 715)
@@ -1,3 +1,2 @@
-#define VERSION "0.1-9d"
-#define DATE "October 08, 2010"
-
+#define VERSION "0.1-9e"
+#define DATE "May 15, 2011"
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