[Genabel-commits] r1177 - in pkg/GenABEL: . R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 2 18:29:00 CEST 2013
Author: lckarssen
Date: 2013-04-02 18:29:00 +0200 (Tue, 02 Apr 2013)
New Revision: 1177
Modified:
pkg/GenABEL/CHANGES.LOG
pkg/GenABEL/R/export.plink.R
Log:
Change the default for export.plink() to write transposed ped files (.tped/.tfam). This works around bug #2055.
Modified: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG 2013-04-02 16:10:59 UTC (rev 1176)
+++ pkg/GenABEL/CHANGES.LOG 2013-04-02 16:29:00 UTC (rev 1177)
@@ -1,8 +1,14 @@
+*** v.
+
+(2013.04.02)
+Changed default behaviour of the export.plink() version. Export to .tped is now
+the default (because of the bugginess of the .ped export, see bug #2055.
+
*** v. 1.7-4 (2013.02.22)
(2013.02.22)
-replacing SNP with get("SNP") in impute2databel with option 'old' so to avoid
-CRAN checks complains
+replacing SNP with get("SNP") in impute2databel with option 'old' so to avoid
+CRAN checks complains
(2013.02.03)
Fixing bug in 'grammar': when using 'gamma', effects and s.e.s are not re-computed
@@ -22,32 +28,32 @@
(2013.01.07)
Fixing the problem which prevents the package from loading while checking the version on CRAN
-(2012.12.03, YA)
-- Changes in DESCRIPTION and version to denote new working
+(2012.12.03, YA)
+- Changes in DESCRIPTION and version to denote new working
version
-- added argument 'eigenOfRel' to 'polygenic' allowing passing
-the results of 'eigen' of the relationship matrix instead of the matrix
-itself (makes much faster evaluation). See unit test test.polygenic.eigenOfRel
+- added argument 'eigenOfRel' to 'polygenic' allowing passing
+the results of 'eigen' of the relationship matrix instead of the matrix
+itself (makes much faster evaluation). See unit test test.polygenic.eigenOfRel
for use example
-- found out that impute2databel is broken, see bug report [#2418]
+- found out that impute2databel is broken, see bug report [#2418]
*** v. 1.7-2 (2012.10.14)
-(2012.09.14, YA)
+(2012.09.14, YA)
Changes in DESCRIPTION and version
(2012.08.29, YA)
-Small changes related to CRAN release of 1.7-1; this release is to be
-updated to 1.7-2 as soon as the Grammar-Gamma paper is published and
+Small changes related to CRAN release of 1.7-1; this release is to be
+updated to 1.7-2 as soon as the Grammar-Gamma paper is published and
some feedback is collected for the 1.7-1
(2012.08.15, YA)
-Small updates to documentation, verifying that checks are passed.
-Many NOTEs about use of partial arguments - something to fix
-eventually.
+Small updates to documentation, verifying that checks are passed.
+Many NOTEs about use of partial arguments - something to fix
+eventually.
(2012.08.09, YT)
@@ -61,83 +67,83 @@
*** v. 1.7-1 (2012.04.27)
-Replaced 'grammar' function with new one, allowing 'raw', 'gc'
+Replaced 'grammar' function with new one, allowing 'raw', 'gc'
and 'gamma' varieties of the method.
-Added option weight = "eVar" to 'ibs'. This uses empirical variance of
-genotypes when estimating kinship matrix. This is useful when working with
-such data as Arabidopsis.
+Added option weight = "eVar" to 'ibs'. This uses empirical variance of
+genotypes when estimating kinship matrix. This is useful when working with
+such data as Arabidopsis.
*** v. 1.7-0 (2011.12.20)
-Addressed bug [#1383] (message about upgrade on loading the library
-not entirely correct) by adding new function checkPackageVersionOnCRAN()
-and re-writing zzz.R (.onLoad) using it.
+Addressed bug [#1383] (message about upgrade on loading the library
+not entirely correct) by adding new function checkPackageVersionOnCRAN()
+and re-writing zzz.R (.onLoad) using it.
-Addressed bug [#1673] (bug in load.gwaa.data and export.merlin when
-sorting is enabled, filed in by Daniel Taliun), added unit test
+Addressed bug [#1673] (bug in load.gwaa.data and export.merlin when
+sorting is enabled, filed in by Daniel Taliun), added unit test
runit.sortmap.internal.R/test.sortmap.internal.bug1673
-Addressed bug [#1676] (regression in merge of gwaa.data, phenotypes
-don't get merged correctly; filed in by Lennart Karssen), added unit
+Addressed bug [#1676] (regression in merge of gwaa.data, phenotypes
+don't get merged correctly; filed in by Lennart Karssen), added unit
test runit.merge.R/test.merge.bug1676
-Added 'KS' method to estimate lambda in 'estlambda'. Generates rather
-good results (under null) and may be considered as default option in the future,
-after testing under the alternative.
+Added 'KS' method to estimate lambda in 'estlambda'. Generates rather
+good results (under null) and may be considered as default option in the future,
+after testing under the alternative.
-Account for situation when HGLM fails to converge (s.e.'s set to NA in
-h2$h2an$se)
+Account for situation when HGLM fails to converge (s.e.'s set to NA in
+h2$h2an$se)
added option 'transposed' to 'export.plink' to export TPED files
-speeding-up 'mmscore' by x1.8 through more efficient vector-matrix
-product computations
+speeding-up 'mmscore' by x1.8 through more efficient vector-matrix
+product computations
export.merlin, export.plink now runs much faster (exports on C++ code)
-Bug [#1641] (regression bug with merge.snp.data in version 1.6.9;
-filed in by Karl Froner) fixed. Now GenABEL deals with exceptional
-situation in merge.snp.data / monomorphic part; added case of no overlap
-in SNPs (skip monomorphic staff then). RUnit regression test
-runit.merge.R/test.merge.bug1641 added.
+Bug [#1641] (regression bug with merge.snp.data in version 1.6.9;
+filed in by Karl Froner) fixed. Now GenABEL deals with exceptional
+situation in merge.snp.data / monomorphic part; added case of no overlap
+in SNPs (skip monomorphic staff then). RUnit regression test
+runit.merge.R/test.merge.bug1641 added.
-Modifications in 'estlambda': plot=FALSE by default, added option
-to estimate Lambda with median method; added option 'filter' for
+Modifications in 'estlambda': plot=FALSE by default, added option
+to estimate Lambda with median method; added option 'filter' for
filtering SNPs with 0-statistics
*** v. 1.6-9 (2011.08.30)
-Change the name of 'maintainer' to genabel.project at gmail.com to avoid spamming
+Change the name of 'maintainer' to genabel.project at gmail.com to avoid spamming
CRAN people
*** v. 1.6-8 (2011.08.25)
added 'strand<-' method for snp.data and gwaa.daat-class
-added 'id' argument to 'load.gwaa.daat'. This may be handy when eg
+added 'id' argument to 'load.gwaa.daat'. This may be handy when eg
importing PLINK phenotypic data id="IID"
Update of 'polygenic_hglm' by Xia Shen. Quote:
-We've updated the hglm package to version 1.2-2 recently on CRAN, where
+We've updated the hglm package to version 1.2-2 recently on CRAN, where
the major updates include:
- Sparse matrix implementation
- Multiple random effects
- Function hglm2() which accepts lme4-style formula input
-In this update of polygenic_hglm() the speed could be slightly faster than
-before since the hglm() now uses sparse matrix technique (however I don't
-expect it to be much faster since the kinship matrix is always dense). Other
+In this update of polygenic_hglm() the speed could be slightly faster than
+before since the hglm() now uses sparse matrix technique (however I don't
+expect it to be much faster since the kinship matrix is always dense). Other
modifications are:
-- The current update of hglm package does not spit out profile log-likelihood
-since we haven't perfectly solved the likelihood computation for multiple random
-effects yet. But since polygenic_hglm() only needs one random effect (polygenic
-effect), I've re-implemented the likelihood computation directly in
+- The current update of hglm package does not spit out profile log-likelihood
+since we haven't perfectly solved the likelihood computation for multiple random
+effects yet. But since polygenic_hglm() only needs one random effect (polygenic
+effect), I've re-implemented the likelihood computation directly in
polygenic_hglm(), and no need to specify 'method = "REML"' anymore.
-- In order to solve the problem from the forum about inputting formula as
-'y' or 'y ~ 1', I've added a check before creating the model.frame, so now
+- In order to solve the problem from the forum about inputting formula as
+'y' or 'y ~ 1', I've added a check before creating the model.frame, so now
both types of inputs should work.
-Added 'recodeChromosome' function, which must be handy when e.g. importing data
+Added 'recodeChromosome' function, which must be handy when e.g. importing data
from other software which uses integer for sex chromosomes and other non-autosomes
(X, Y, mt).
@@ -147,49 +153,49 @@
Updated documentation for 'scan.glm.2D'.
-Added GRAMMAR+ transformation and computation of GRAMMAR+
+Added GRAMMAR+ transformation and computation of GRAMMAR+
correction factors to 'polygenic'.
-The default value for the stand option to convert.snp.tped() is now "u",
-instead of "+". Now convert.snp.tped() and convert.snp.ped() have the
+The default value for the stand option to convert.snp.tped() is now "u",
+instead of "+". Now convert.snp.tped() and convert.snp.ped() have the
same defaults.
-Added patch of bug [#1322] + regression test (contributed
-by Nicola Pirastu, see
-https://lists.r-forge.r-project.org/pipermail/genabel-devel/2011-May/000276.html).
-This is still suboptimal treatment -- the covariate is just dropped;
-in say 'lm' it is 'kept' with NA as estimate, and IDs with missing
+Added patch of bug [#1322] + regression test (contributed
+by Nicola Pirastu, see
+https://lists.r-forge.r-project.org/pipermail/genabel-devel/2011-May/000276.html).
+This is still suboptimal treatment -- the covariate is just dropped;
+in say 'lm' it is 'kept' with NA as estimate, and IDs with missing
data dropped, which is not the case with 'polygenic'.
-Speeding up 'polygenic' by avoiding multiple inverses of
+Speeding up 'polygenic' by avoiding multiple inverses of
the matrix.
-Fixed bug in 'polygenic' causing the offset in
-names(...$residualY) and names(...$pgresidualY) in
-case of missing observations.
+Fixed bug in 'polygenic' causing the offset in
+names(...$residualY) and names(...$pgresidualY) in
+case of missing observations.
-Updated the merge.snp.data procedure to allow meaningful
-merging of mono- and poly- codings. Take care -- this is
-new and not tested much yet! You best check few results
+Updated the merge.snp.data procedure to allow meaningful
+merging of mono- and poly- codings. Take care -- this is
+new and not tested much yet! You best check few results
manually after the merge!
Added coding<- method to gwaa.data and snp.data classes
-Added I/D encoding and monomorphic classes (AA, TT, GG, CC,
+Added I/D encoding and monomorphic classes (AA, TT, GG, CC,
--, II, DD, ...) to 'snp.data' and convert.snp.*
-Updated 'polygenic' with use of 'polylik_eigen' developed by
-Gulnara Svischeva. Now 'polygenic' works MUCH faster. The
-main advantage of Gulnara's method is that time to compute
-the likelihood function is approximately linear with number
-of subjects. In that, relative speed-up grows with sample
-size growth, e.g. for 100 IDs, it is x15, x40 for 200,
-x60 for 400, and xX for 800 individuals (using two fixed effect
-covariates, see runit.polylik.R). Also added RUnit test to check
-consistency of results based on old 'polylik' and new
+Updated 'polygenic' with use of 'polylik_eigen' developed by
+Gulnara Svischeva. Now 'polygenic' works MUCH faster. The
+main advantage of Gulnara's method is that time to compute
+the likelihood function is approximately linear with number
+of subjects. In that, relative speed-up grows with sample
+size growth, e.g. for 100 IDs, it is x15, x40 for 200,
+x60 for 400, and xX for 800 individuals (using two fixed effect
+covariates, see runit.polylik.R). Also added RUnit test to check
+consistency of results based on old 'polylik' and new
'polylik_eigen'.
-Upgrade version number
+Upgrade version number
*** v. 1.6-7 (2011.05.17)
@@ -200,8 +206,8 @@
Fixed 'technical' bug [1398] (related to changes in R 2.14):
https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1398&group_id=505&atid=2058
-Set 'GenABEL developers' as a maintainer of the package;
-set the genabel-devel list as 'maintainer' e-mail
+Set 'GenABEL developers' as a maintainer of the package;
+set the genabel-devel list as 'maintainer' e-mail
Fixing bug [1388], added regression test
https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1388&group_id=505&atid=2058
@@ -212,63 +218,63 @@
*** v. 1.6-6 (2011.04.29)
-Added Xia Shen's procedure 'polygenic_hglm'. Features: quick
+Added Xia Shen's procedure 'polygenic_hglm'. Features: quick
convergence, standard errors for fixed effects.
-Updated check.marker, added warning if no. Y-markers is < 10
+Updated check.marker, added warning if no. Y-markers is < 10
-Applied the patch of Nicola Pirastu
+Applied the patch of Nicola Pirastu
http://lists.r-forge.r-project.org/pipermail/genabel-devel/2011-March/000182.html
-to descriptives.trait. Added RUnit regression tests, updated
+to descriptives.trait. Added RUnit regression tests, updated
documentation. Bugs fixed: [#1184], [#1185], [#1259]
-Added 'reconstructNPs' function; added extra options
-to 'findRelatives'.
+Added 'reconstructNPs' function; added extra options
+to 'findRelatives'.
-Added a number of functions facilitating relationship checks.
-The core function is 'findRelatives'. Compared
-to guessing relations from genomic kinship matrix, this
-procedure offers several enhancements: (1) by use of IBD/IBS
-3-state space, it allows to distinguish between some pairs,
-which have the same kinship (e.g. parent-offspring from
-brother-sister; uncle-nephew from grandparent-grandchild, etc.)
+Added a number of functions facilitating relationship checks.
+The core function is 'findRelatives'. Compared
+to guessing relations from genomic kinship matrix, this
+procedure offers several enhancements: (1) by use of IBD/IBS
+3-state space, it allows to distinguish between some pairs,
+which have the same kinship (e.g. parent-offspring from
+brother-sister; uncle-nephew from grandparent-grandchild, etc.)
(2) it reports likelihood, allowing for more rigorous inferences
-Changes in convert.snp.mach documentation to reflect the fact that
-the map-file should have header; changes to convert.snp.illumina
-documentation to reflect the nature of the data better; added
+Changes in convert.snp.mach documentation to reflect the fact that
+the map-file should have header; changes to convert.snp.illumina
+documentation to reflect the nature of the data better; added
option 'mapHasHeaderLine' to convert.snp.ped and updated documentation
-(resolving feature request #1317).
+(resolving feature request #1317).
***** v. 1.6-5 (2011.02.07)
-Added '#include <cstdarg>' to iterator.cpp to solve
+Added '#include <cstdarg>' to iterator.cpp to solve
'[#1273] GenABEL 1.6-5 does not compile'
-commented S4methods... in NAMESPACE to meet the
-request from the R-team; patched documentation for
-summary.scan.gwaa and summary.gwaa.data
-in order to avoid NOTE about S3methods "usage"
+commented S4methods... in NAMESPACE to meet the
+request from the R-team; patched documentation for
+summary.scan.gwaa and summary.gwaa.data
+in order to avoid NOTE about S3methods "usage"
section
-added extra checks for impute2databel to ensure that
+added extra checks for impute2databel to ensure that
sample file header is not used
-change in merge.snp.data by Maksim Struchalin, adding option
-"intersected_snps_only" (if TRUE, then only interesected SNPs
+change in merge.snp.data by Maksim Struchalin, adding option
+"intersected_snps_only" (if TRUE, then only interesected SNPs
will be in output)
-Disabled check on intermediateXF in check.marker by setting intermediateXF=c(.5,.5)
-by default. This will be dealt with further (see tracker '[#1210] intermediate
-inbreeding checks with check.marker' )
+Disabled check on intermediateXF in check.marker by setting intermediateXF=c(.5,.5)
+by default. This will be dealt with further (see tracker '[#1210] intermediate
+inbreeding checks with check.marker' )
patched Roxygen documentation for qtscore
use of 'setTxtProgressBar' in qtscore with times > 1 to indicate progress
-polygenic() added default option patchBasedOnFGLS, if no convergence based
-on difFGLS criterion, fixed effect betas are patched to FGLS betas before
-starting re-iteration
+polygenic() added default option patchBasedOnFGLS, if no convergence based
+on difFGLS criterion, fixed effect betas are patched to FGLS betas before
+starting re-iteration
adding a wrapper chi2_CG -> cocohet
@@ -284,8 +290,8 @@
added mechanism to check for updates at load time
-moved summary.snp.data to 'iterator' framework, changes in gwaa.data at gtdata@gtps
-definition, now 'ANY' allowing for use of different types of data with
+moved summary.snp.data to 'iterator' framework, changes in gwaa.data at gtdata@gtps
+definition, now 'ANY' allowing for use of different types of data with
interator. Interestingly, for 'old' data type computations became faster!
@@ -297,13 +303,13 @@
***** v. 1.6-3 (2010.08.14)
-changes in the code and tutorial due to preparing
+changes in the code and tutorial due to preparing
for ESP29 course
added function 'export.plink'
-added multiple methods to work with 'gwaa.data', 'snp.data' and
-'scan.gwaa classes, such as 'annotation', 'coding', 'refallele',
+added multiple methods to work with 'gwaa.data', 'snp.data' and
+'scan.gwaa classes, such as 'annotation', 'coding', 'refallele',
'effallele', ...
more annotations are delivered for summary objects
@@ -314,21 +320,21 @@
***** v. 1.6-0 (2010.06.21)
-changes in DatABEL-embed functions used by impute2databel (treating of NAs);
+changes in DatABEL-embed functions used by impute2databel (treating of NAs);
added tests for that situation
***** v. 1.5-9 (2010.06.18)
change in DESCRIPTION anyDuplicated() is in R 2.10.0, but not in 2.4.0
-small changes in polygenic -- convergence checks with intercept-only model; treatment
+small changes in polygenic -- convergence checks with intercept-only model; treatment
for h2-boundary-stick situations (at small N)
***** v. 1.5-8 (2010.06.10)
-multiple changes in polygenic default parameters
-and extra criteria now allowing better
-convergence. Many thanks to Nicola Pirastu for spotting
+multiple changes in polygenic default parameters
+and extra criteria now allowing better
+convergence. Many thanks to Nicola Pirastu for spotting
poor convergence when multiple parameters were estimated!
added methods "dim" and "dimnames" to snp.data-class
@@ -341,7 +347,7 @@
***** v. 1.5-4 (2010.05.09)
-changes in filevector related to DatABEL not passing checks on Windows
+changes in filevector related to DatABEL not passing checks on Windows
(disconnect used FiltredMatrix destructor, which does not call AbstractMatrix destructor)
***** v. 1.5-2 (2010.05.04)
@@ -368,8 +374,8 @@
***** v. 1.4-9 (2010.02.06)
-added arrange_probabel_phe(), also shortcuts to
-slots of gwaa.data-class: chromosome, coding,
+added arrange_probabel_phe(), also shortcuts to
+slots of gwaa.data-class: chromosome, coding,
gtdata, idnames, map, nids, nsnps, phdata, snpnames, strand
***** v. 1.4-8 (2010.01.24)
@@ -382,8 +388,8 @@
cleaned help for polygenic()
-Diagonal elements returned by ibs(...,w="freq") changed from (0.5+F) to
-0.5*(1+F) (thanks to Chris Haley for pointing this problem out!)
+Diagonal elements returned by ibs(...,w="freq") changed from (0.5+F) to
+0.5*(1+F) (thanks to Chris Haley for pointing this problem out!)
***** v. 1.4-6 (2009.11.06)
@@ -391,34 +397,34 @@
***** v. 1.4-5 (2009.09.09)
-New function "var.meta" added.
-Function is intended for pooling (meta-analysing) trait means for
-different genotypes separately.Input files have to be like in example
+New function "var.meta" added.
+Function is intended for pooling (meta-analysing) trait means for
+different genotypes separately.Input files have to be like in example
-below (plink generate this kind of files). At the end you have one file
+below (plink generate this kind of files). At the end you have one file
in same format but with pooled MEANs and SDs
***** v. 1.4-4 (2009.09.02)
-bug fix in hom() and perid.summary() -- only polymorphic markers were used to
+bug fix in hom() and perid.summary() -- only polymorphic markers were used to
report call rate etc. Many thanks to Patrice Godard, who has reported the bug!
-The bug only appeared in version 1.4-3
+The bug only appeared in version 1.4-3
project submitted to r-forge
***** v. 1.4-3 (2009.07.21)
qvalue moved to "suggests"; no strict dependency on availability of that anymore
-(thanks to Beate Glaser for noting that tcltk is not so obvious component
+(thanks to Beate Glaser for noting that tcltk is not so obvious component
of all systems)
changes to C++ LM code to improve portability (Solaris 10)
-hom() function updated, now producing variances (to be used as diagonal
+hom() function updated, now producing variances (to be used as diagonal
elements of the genomic kinshp matrix when doing EIGENSTRAT analysis).
Many thanks to John Barnard for contributing the code!
-all class checks changed to ensure compatibility with S4
+all class checks changed to ensure compatibility with S4
(thanks to Maxime Rotival)
@@ -428,19 +434,19 @@
***** v. 1.4-2 (2009.01.28)
-Changes in polygenic()/mmscore() to allow for sub-setting on
+Changes in polygenic()/mmscore() to allow for sub-setting on
IDs
-Bug fix in mmscore(). The bug concernes estimates of beta, the
-P-values reported by mmscore() were not affected.
+Bug fix in mmscore(). The bug concernes estimates of beta, the
+P-values reported by mmscore() were not affected.
***** v. 1.4-1 (2008.11.26)
-merge.gwaa.data, merge.snp.data well tested and
-recommended for wider use (special thanks to Arne
+merge.gwaa.data, merge.snp.data well tested and
+recommended for wider use (special thanks to Arne
Schillert and Michael Preuss)
-Modifications of some functions for better parallelizability.
+Modifications of some functions for better parallelizability.
[user-invisible] changes to: ibs, hom, r2fast, perid.summary
(thanks to Surakameth Mahasirimongkol and Unitsa Sangket)
@@ -448,15 +454,15 @@
(thanks to many people reporting the problem)
Partly resolving incompatibility between the way GenABEL
-computes the diagonal elemnts of the "covariance matrix"
-for use in egscore() and the original EIGENSTRAT matrix
+computes the diagonal elemnts of the "covariance matrix"
+for use in egscore() and the original EIGENSTRAT matrix
(many thanks to Guiseppe Palermo)
***** v 1.4-0e (2008.09.18)
Small changes in mlreg for consistency to formetascore required input
-Bug fix in mlreg (would produce meaningful results when no. snps is
+Bug fix in mlreg (would produce meaningful results when no. snps is
dividable by 4)
***** v 1.4-0d (2008.08.21)
@@ -471,15 +477,15 @@
Multiple fixes in merge.snp.data
-Fix in check.marker (for Y-chromosome, the call rate
+Fix in check.marker (for Y-chromosome, the call rate
was estimated using all people)
***** v 1.3-9 (2008.04.23)
-Function mlreg() (aka reg.gwaa()) added. Implements maximum likelihood
-estimation and Wald test for linear and logistic regression and Cox
-proportional hazards models.
+Function mlreg() (aka reg.gwaa()) added. Implements maximum likelihood
+estimation and Wald test for linear and logistic regression and Cox
+proportional hazards models.
Function convert.snp.affymetrix() added
@@ -489,7 +495,7 @@
Modifications to formetascore() (now can run with mmscore())
-Few cleanups
+Few cleanups
***** v 1.3-6 (2008.03.20)
@@ -506,35 +512,35 @@
***** v 1.3-5c (2008.02.27)
-Bug fix in check.maker.internal (with "lower" option, would not exclude
+Bug fix in check.maker.internal (with "lower" option, would not exclude
on IBS).
-Small bug fix estlambda (would not run if supplied with P-values, and
+Small bug fix estlambda (would not run if supplied with P-values, and
some P-values are < 1.e-16). This bug did not affect any other function.
***** v 1.3-5b (2008.02.21)
-Bug fix in ztransform(): would not work without data argument,
+Bug fix in ztransform(): would not work without data argument,
if formula supplied will not use it. This bug also affected rntransform().
***** v 1.3-5 (2008.02.15)
qtscore "binomial" workout
-minor bug fix in check.marker() -- the procedure would fail to run
+minor bug fix in check.marker() -- the procedure would fail to run
in presence of more than couples of "twin" (e.g. multiple plant clones).
-bug fix in formetascore() function: standard errors were reported with
+bug fix in formetascore() function: standard errors were reported with
sign of beta
***** v 1.3-3d (2008.02.11)
-A fix in npsubtreated() function (in some situations all medicated
+A fix in npsubtreated() function (in some situations all medicated
people's values were set to NA)
***** v 1.3-3c (2008.02.03)
-npsubtreated() function, to be used in analysis of
+npsubtreated() function, to be used in analysis of
traits affetcted by treatment (medication) added.
formetascore() procedure extended with parameter "verbosity".
@@ -546,132 +552,132 @@
Y and mtDNA markers-specific analyses added in QC function check.marker()
This also involves checks for people with XXY genotypes.
-Robust Genomic Control added to correct 2df test in qtscore
+Robust Genomic Control added to correct 2df test in qtscore
function -- yet experimental.
-formetascore() function introduced -- analysis oriented to
+formetascore() function introduced -- analysis oriented to
future meta-analysis.
-ztransform function created, rntransform function modified to take
+ztransform function created, rntransform function modified to take
similar syntax as ztransform.
-Bug in convert.snp.merlin (similar to the one in convert.snp.illumina)
+Bug in convert.snp.merlin (similar to the one in convert.snp.illumina)
fixed.
***** v 1.3-2 (2007.12.18)
-Extensive cleanup, including fixes to mmscore and grammar;
+Extensive cleanup, including fixes to mmscore and grammar;
examples introduced for polygenic, mmscore, grammar, and others.
-Bug in convert.snp.tped (similar to the one in convert.snp.illumina)
+Bug in convert.snp.tped (similar to the one in convert.snp.illumina)
fixed.
-The number of people/genotypes (N) used in analysis of a particular SNP
+The number of people/genotypes (N) used in analysis of a particular SNP
added to the output of qtscore, mmscore, ccfast, egscore, and grammar.
-plot.scan.gwaa changed -- now it is possible to use ylim.
+plot.scan.gwaa changed -- now it is possible to use ylim.
-Bug fix in qtscore with binary traits without covariates -- there was
+Bug fix in qtscore with binary traits without covariates -- there was
no test whether coding is 0/1 (if not, test would be wrong).
-Changes in C code of concerns functions convert.snp.mach and
-convert.snp.ped. Speed of conversion from MACH format greatly
+Changes in C code of concerns functions convert.snp.mach and
+convert.snp.ped. Speed of conversion from MACH format greatly
improved.
***** v 1.3-1 (2007.11.05)
-The strand information as based on build 35, is available from Yurii
-for Illumina 318K.
+The strand information as based on build 35, is available from Yurii
+for Illumina 318K.
-Bug fix in convert.snp.illumina (alleles would change to the other one
+Bug fix in convert.snp.illumina (alleles would change to the other one
in large proportion of SNPs, e.g. A/G polymorphism, AA -> GG, GG -> AA).
-Though this does not affect results directly (e.g. P-values and the absolute
-effect values are OK), this may couse confusion when you compare your
-results to other people's results (the sign of the effect may be swapped),
-also imputations would have gone wrong.
+Though this does not affect results directly (e.g. P-values and the absolute
+effect values are OK), this may couse confusion when you compare your
+results to other people's results (the sign of the effect may be swapped),
+also imputations would have gone wrong.
Small bug fixes with strand operations (SNP names were lost in sub-setting).
-New procedure rntransform(). This procedure performs
-rank transformation to normality. The transformed variable
-is perfectly normal, unless there are ties in the original
+New procedure rntransform(). This procedure performs
+rank transformation to normality. The transformed variable
+is perfectly normal, unless there are ties in the original
distribution.
***** v 1.2-9 (2007.10.22)
-A bug fix in check.markers(ibs.exclude="lower") -- before the fix, the
+A bug fix in check.markers(ibs.exclude="lower") -- before the fix, the
samples with HIGHER call were excluded. Thanks to Tuuli Lappalainen!
Bug fix in refresh.gwaa.data
option "details" added to qtscore().
-When details=FALSE, SNP and ID names
+When details=FALSE, SNP and ID names
are not reported, which saves some memory
***** v 1.2-8 (2007.08.27)
-GenABEL tutorial updated and, internals joined with
+GenABEL tutorial updated and, internals joined with
tutorial, new introductory sections added.
-New association analysis procedure introduced.
-egscore() computes association statistics adjusted
+New association analysis procedure introduced.
+egscore() computes association statistics adjusted
for eigenvector(s), following Price et al, Nat. Genet.,
-2006.
+2006.
-Improved and new functionality of check.marker():
-much faster X-errors check, identification of female
-which are likely to be male. When "twin" DNAs are
-identified, the one with lower call may be dropped,
+Improved and new functionality of check.marker():
+much faster X-errors check, identification of female
+which are likely to be male. When "twin" DNAs are
+identified, the one with lower call may be dropped,
or both (previously random).
***** v 1.2-7 (2007.08.13)
-New list names added to output produced by qtscore(),
-grammar(), ccfast() and mmscore(): chi2.1df and
-chi2.2df. These correspond to Chi-square values produced.
+New list names added to output produced by qtscore(),
+grammar(), ccfast() and mmscore(): chi2.1df and
+chi2.2df. These correspond to Chi-square values produced.
The minimal P-values, as before, are resti=ricted to 1e-16
-Improvements in plot.scan.gwaa() and add.plot() --
-now 0-probabilities converted to 1.e-16 (previously
-a warning message would be produced and the point would be
-dropped); also option df="Pc1df" introduced.
+Improvements in plot.scan.gwaa() and add.plot() --
+now 0-probabilities converted to 1.e-16 (previously
+a warning message would be produced and the point would be
+dropped); also option df="Pc1df" introduced.
-***** v 1.2-6 (2007.08.08)
+***** v 1.2-6 (2007.08.08)
A major improvement in GenABEL ability to import and export data
-compatible in format to other packages and databases.
+compatible in format to other packages and databases.
-NOTE: to convert your R data from old to new format within R, use
-refresh.gwaa.data() function. Old phenotype- and genotype- files will load
+NOTE: to convert your R data from old to new format within R, use
+refresh.gwaa.data() function. Old phenotype- and genotype- files will load
with load.gwaa.data with no problem.
-One of the main goals behind this effort was to make GW imputations
+One of the main goals behind this effort was to make GW imputations
with MACH software (G. Abecasis) easy.
-(a) New format of GenABEL data (0.1) developed. Now the
- features stored by GenABEL include SNP coding (actual nucleotides)
- and strand.
+(a) New format of GenABEL data (0.1) developed. Now the
+ features stored by GenABEL include SNP coding (actual nucleotides)
+ and strand.
-(b) New and updated convert.snp.* functions, which convert genotypic
+(b) New and updated convert.snp.* functions, which convert genotypic
data from external to GenABEL format
- -- convert.snp.ped: large improvement in speed (now in C++),
- flexible control. Pre-makeped, MERLIN
- and MACH formats supported
+ -- convert.snp.ped: large improvement in speed (now in C++),
+ flexible control. Pre-makeped, MERLIN
+ and MACH formats supported
-- convert.snp.tped: some bug fixes, switch to 0.1 data format
-- convert.snp.mach (NEW!): converts MACH files to GenABEL
- format, allowing for filtering on
- quality
+ format, allowing for filtering on
+ quality
- -- convert.snp.illumina (NEW!): converter for Affymetrix / Illumina
- style of files
+ -- convert.snp.illumina (NEW!): converter for Affymetrix / Illumina
+ style of files
-(c) export.merlin() function to export data in MERLIN format. MACH
- can be directly applied on these files. Coupled with
- convert.snp.ped(format="mach") this allows easy data export,
- imputations, and re-import.
+(c) export.merlin() function to export data in MERLIN format. MACH
+ can be directly applied on these files. Coupled with
+ convert.snp.ped(format="mach") this allows easy data export,
+ imputations, and re-import.
***** v 1.2-5 (2007.07.11)
@@ -682,29 +688,29 @@
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1177
More information about the Genabel-commits
mailing list