[Genabel-commits] r1321 - in pkg/GenABEL: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Aug 27 21:24:17 CEST 2013
Author: yurii
Date: 2013-08-27 21:24:17 +0200 (Tue, 27 Aug 2013)
New Revision: 1321
Added:
pkg/GenABEL/ChangeLog
Removed:
pkg/GenABEL/CHANGES.LOG
Modified:
pkg/GenABEL/DESCRIPTION
pkg/GenABEL/R/impute2databel.R
pkg/GenABEL/R/mmscore.R
pkg/GenABEL/R/zzz.R
pkg/GenABEL/man/mmscore.Rd
Log:
excluding version checks + "fixing" warnings produced by R CMD check --as-cran
Deleted: pkg/GenABEL/CHANGES.LOG
===================================================================
--- pkg/GenABEL/CHANGES.LOG 2013-08-26 13:27:52 UTC (rev 1320)
+++ pkg/GenABEL/CHANGES.LOG 2013-08-27 19:24:17 UTC (rev 1321)
@@ -1,966 +0,0 @@
-*** v. 1.7-7
-
-(2013.07.19)
-Added warning that *2databel's may not produce output in desired data type
-and fall onto float
-
-(2013.06.29)
-Changed the 'polygenic' nullification threshold to 1e-8
-
-Added references for Grammar+ transformation
-
-Allowed for user-specified output data type in '*2databel' functions
-
-Changed version number to 1.7-7
-
-(2013.06.06)
-Two new functions added: LiLog() and palinear2LiLog() for the
-estimation of logistic beta's from a linear regression. Thanks to
-Nicola Pirastu for this contribution. The paper that describes these
-methods has been submitted (see the help of both functions for the
-citation).
-
-(2013.06.03)
-Fixed bug #2664 in export.merlin() (exported files differ when using
-different settings for the stepids argument).
-
-(2013.05.30)
-Fixed memory leak in export.plink() when exporting to .ped format (Bug #2055).
-
-*** v. 1.7-6
-
-(2013.05.16)
-Negative eigenvalues set to 'very small' (1e-16) instead using abs
-in 'polygenic': this is more justified
-Fixed too long lines in Rd files.
-
-(2013.05.15)
-Updated version number to 1.7-6 (release), checked with latest
-dev-version of R available. Added 'bigRR' as suggested package.
-
-*** v. 1.7-5
-
-(2013.04.09)
-Fixing bug [#2672] (GenABEL::cocohet default graph output). Now by
-default the function does not produce graphics (makePlot = FALSE); if
-graphics is requested (makePlot = TRUE) it is produced using a default
-plot device (so a user can redirect the output to a file if (s)he
-desires and in the way (s)he desires).
-
-(2013.04.04)
-Fixing bug [#2525] (http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2525&group_id=505&atid=2058)
-Thanks to Vladimir Naumov for submitting the patch!
-
-Updated documentation files
-
-(2013.04.03)
-Added patch to bug [#1287] - example(ibs) producing strange clusters.
-Thanks to Vladimir Naumov for submitting the patch!
-
-(2013.04.03)
-Upgraded the version number to 1.7-5
-
-(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
-
-(2013.02.03)
-Fixing bug in 'grammar': when using 'gamma', effects and s.e.s are not re-computed
-(bug reported by Xia Shen)
-
-(2013.01.18)
-Fixing bug in ztransform (if NA is present and formula used, NA's are kicked out)
-Changed the version number
-
-*** v. 1.7-3 (2013.01.09)
-
-(2013.01.09)
-Commented the parts related to non-additive GC in qtscore
-Removed calls to 'attach' from multiple procedures
-Decrease of running time for long-running examples (GC_ovdom,GC,check.marker,Xfix,srdta)
-
-(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
-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
-for use example
-- found out that impute2databel is broken, see bug report [#2418]
-
-*** v. 1.7-2 (2012.10.14)
-
-(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
-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.
-
-(2012.08.09, YT)
-
-Add new function GC (Genomic control for non-additive models) and GC_ovdom fot overdominant model.
-Update some functions.
-
-(2012.07.06, YT)
-
-Removed documentation file grammar.old.Rd as obsolete
-Add new function PGC (Polynomial genomic control for non-additive models)
-
-*** v. 1.7-1 (2012.04.27)
-
-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.
-
-*** 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 [#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
-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.
-
-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
-
-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.
-
-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
-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
-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
-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
-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
-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
- both types of inputs should work.
-
-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).
-
-+> tutorial genetic data QC - list all options, do not use default?
-
-'check.marker' added "none" (equal to ibs.mrk = -1); set "both" to default
-
-Updated documentation for 'scan.glm.2D'.
-
-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
-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
-data dropped, which is not the case with 'polygenic'.
-
-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.
-
-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,
---, 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
-'polylik_eigen'.
-
-Upgrade version number
-
-*** v. 1.6-7 (2011.05.17)
-
-Submitted 1.6-7, based on r727, to CRAN
-
-Deleting some pdf from 'doc' and compressing 'data'
-
-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
-
-Fixing bug [1388], added regression test
-https://r-forge.r-project.org/tracker/index.php?func=detail&aid=1388&group_id=505&atid=2058
-
-upgrade version number
-
-fix in example of polygenic_hglm
-
-*** v. 1.6-6 (2011.04.29)
-
-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
-
-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
-documentation. Bugs fixed: [#1184], [#1185], [#1259]
-
-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.)
-(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
-option 'mapHasHeaderLine' to convert.snp.ped and updated documentation
-(resolving feature request #1317).
-
-***** v. 1.6-5 (2011.02.07)
-
-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"
-section
-
-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
-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' )
-
-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
-
-adding a wrapper chi2_CG -> cocohet
-
-fixed 'demo(ge03d2)'
-
-'stepids' argument added to export.merlin
-
-Fan/Maksim's procedure for cocohet (CCH) procedure added, renamed by Yurii
-
-Bug fix in export.plink() thanks to Nadya Belonogova
-
-Made sure that SE reported does not carry the sign of beta (always 'abs')
-
-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
-interator. Interestingly, for 'old' data type computations became faster!
-
-
-***** v. 1.6-4 (2010.08.30)
-
-new official release tested by ESP29-2010 participants
-
-many thanks to everybody who provided feedback!
-
-***** v. 1.6-3 (2010.08.14)
-
-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',
-'effallele', ...
-
-more annotations are delivered for summary objects
-
-***** v. 1.6-2 (2010.08.07)
-
-changes due to DatABEL functions names change
-
-***** v. 1.6-0 (2010.06.21)
-
-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
-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
-poor convergence when multiple parameters were estimated!
-
-added methods "dim" and "dimnames" to snp.data-class
-
-***** v. 1.5-6 (2010.05.28)
-
-fixes in filevector
-
-Many thanks to Pau Navarro for help in identification of the bug!
-
-***** v. 1.5-4 (2010.05.09)
-
-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)
-
-switching to new DatABEL with single class
-
-***** v. 1.5-1 (2010.03.17)
-
-further improvement and bug fixes in databel-facilitated functions
-
-***** v. 1.5-0 (2010.03.17)
-
-update of ABEL-tutorial (also few details on NCBI2R added)
-
-general clean-up, submission to CRAN
-
-extended add.phdata()
-
-added del.phdata(), shortcut to @male slot (function male())
-
-added checks for F in sex checks, ...$otherSexErr lists individuals with 0.2 > F > 0.8
-
-multiple changes to xxx2xxx (mach, impute, databel)
-
-***** v. 1.4-9 (2010.02.06)
-
-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)
-
-added export.impute(), patch_strand(), mach2databel(), impute2databel(),
-impute2mach, extract.annotation.impute(), extract.annotation.mach()
-functions
-
-***** v. 1.4-7 (2009.12.03)
-
-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!)
-
-***** v. 1.4-6 (2009.11.06)
-
-Default formetascore's argument transform set to "no"
-
-***** 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
-
-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
-report call rate etc. Many thanks to Patrice Godard, who has reported the bug!
-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
-of all systems)
-
-changes to C++ LM code to improve portability (Solaris 10)
-
-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
-(thanks to Maxime Rotival)
-
-
-***** v. 1.4-2b (2009.02.20)
-
-small fix in merge.gwaa.data (by="id")
-
-***** v. 1.4-2 (2009.01.28)
-
-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.
-
-***** v. 1.4-1 (2008.11.26)
-
-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.
-[user-invisible] changes to: ibs, hom, r2fast, perid.summary
-(thanks to Surakameth Mahasirimongkol and Unitsa Sangket)
-
-Resolved R 2.8.0 issues with load.gwaa.data.
-(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
-(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
-dividable by 4)
-
-***** v 1.4-0d (2008.08.21)
-
-bug fix in merge.snp.data() -- many thanks to Arne Schillert and Michael Preuss
-
-***** v 1.4-0c (2008.07.25)
-
-bug fix in estlambda() -- many thanks to Franz Quehenberger
-
-***** v 1.4-0b (2008.07.21)
-
-Multiple fixes in merge.snp.data
-
-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 convert.snp.affymetrix() added
-
-***** v 1.3-7 (2008.04.16)
-
-Function merge.gwaa.data() added
-
-Modifications to formetascore() (now can run with mmscore())
-
-Few cleanups
-
-***** v 1.3-6 (2008.03.20)
-
-Function merge.snp.data() added
-
-npsubtreated() updated with new functionality
-
-"quality" measure used in convert.snp.mach changed to 7th column (r2)
-
-plot.scan.gwaa(): option df="all" removed, options col, ystart added
-add.plot(): option colors added
-
-Improvement of formetascore function
-
-***** v 1.3-5c (2008.02.27)
-
-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
-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,
-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
-in presence of more than couples of "twin" (e.g. multiple plant clones).
-
-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
-people's values were set to NA)
-
-***** v 1.3-3c (2008.02.03)
-
-npsubtreated() function, to be used in analysis of
-traits affetcted by treatment (medication) added.
-
-formetascore() procedure extended with parameter "verbosity".
-
-***** v 1.3-3 (2008.01.12)
-
-autosomal() function added
-
-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
-function -- yet experimental.
-
-formetascore() function introduced -- analysis oriented to
-future meta-analysis.
-
-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)
-fixed.
-
-***** v 1.3-2 (2007.12.18)
-
-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)
-fixed.
-
-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.
-
-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
-improved.
-
-***** v 1.3-1 (2007.11.05)
-
-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
-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.
-
-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
-distribution.
-
-***** v 1.2-9 (2007.10.22)
-
-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
-are not reported, which saves some memory
-
-***** v 1.2-8 (2007.08.27)
-
-GenABEL tutorial updated and, internals joined with
-tutorial, new introductory sections added.
-
-New association analysis procedure introduced.
-egscore() computes association statistics adjusted
-for eigenvector(s), following Price et al, Nat. Genet.,
-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,
-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.
-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.
-
-***** 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.
-
-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
-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.
-
-(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.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
-
- -- 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.
-
-***** v 1.2-5 (2007.07.11)
-
-Some improvement of convert.snp.ped -- now is able to read
-alleles coded as characters
-
-***** v 1.2-4 (2007.07.10)
-
-Few small fixes done for compatibility with R 2.6.0-devel
-
-convert.snp.tped() procedure by Toby Johnson added.
-This procedure facilitates fast and effective conversion
-from PLINK TPED ("transposed pedigree") format to the
-GenABEL format. See help(convert.snp.tped).
-
-Few other small improvements. This is beta release version
-for procedures facilitating analyses using genomic
-kinship (IBD) matrix, such as polygenic(), mmscore() and
-grammar(). We tested these procedures with quantitative traits
-and they worked fine; for binary traits there may be few
-bugs yet.
-
-***** v 1.2-2 (2007.06.07)
-
-Improvement in polygenic() to ensure convergence, two
-optimisation methods are now allowed.
-
-"Formula" part in qtscore changed to more standard format
-(now one can use any terms allowed in glm, no CRSNP term
-needed).
-
-Bugs in grammar and mmscore fixed. Previous version tended
-to produse some very wrong results.
-
-Polygenic silightly modified (new output objects added).
-A fix in polygenic with covariates.
-
-Other bug fix in stratified analysis with X-chromosome.
-
-***** v 1.2-1 (2007.06.04)
-
-A set of new procedures to do analysis in samples of related
-individuals. They also can be used for analysis of samples
-with population staratification and cryptic relations.
-
-polygenic() provides means to estimate "heritability" and effects
-of covariates, in data having some correlation, as described by
-(genomic) kinship matrix.
-
-Mixed-model score test mmscore() added. This implements the test
-for association between the vector of phenotypes y and vector of genotypes
-g by computing
-
-((y-E[y]) Inverse[V] (g-E[g])^2/((g-E[g]) Inverse[V] (g-E[g])
-
-where Inverse[V] is the inverse of variance-covariance matrix
-and E[y] is expectation of the trait, as provided by polygenic().
-
-grammar() procedure implements fast variant of the above score test
-
-((y-E[y]) Inverse[V] (g-E[g])^2/((g-E[g]) (g-E[g])
-
-This statistics does not have chi-squared distribution, but becomes
-distributed so after GC (thus Pc1df are fine P-values to use)
-
-NOTE: grammar is still experimental.
-
-An error in qtscore, which led to using always only 2 strata
-(male/female) in analysis of X-chromosome fixed.
-
-***** v 1.2-0 (2007.04.17)
-
-Large improvement in the speed of the qvaluebh95() procedure.
-The time used to grow quadratic with the number of P-values to
-evaluate, now reduced to linear.
-
-ibs() procedure "freq" option is updated to provide weighted
-measure of genomic identity.
-
-dprfast() facilitating fast D' computations added. The results
-produced are not exacly the same with D's from LD/genetics.
-
-***** v 1.1-9 (2007.04.04)
-
-A procedure for fast r2 computations (r2fast()) added.
-It seems that this procedure results in r2s which are biased upward
-at small values, compared to r2s from LD/genetics.
-
-A procedure to estimate Morton-Collins rho added (rhofast())
-
-***** v 1.1-8 (2007.03.12)
-
-empirical derivation of GW significance is now embedded into
-qtscore/ccfast, emp.* are now serving as shortcuts to
-call these functions with argument times=100
-
-qtscore: changes to treat binomial variables (residuals from glm)
-
-Added new data sets: ge03d2, ge03d2c
-
-Added demo ge03d2; this ones shows extensive QC + how to deal
-with genetic stratification.
-
-***** v 1.1-7 (2007.03.05)
-
-In scan.haplo.2D procedure with simulate = TRUE change 0s -> 1/(N+1)
-
-add.plot.scan.gwaa() function changed to add.plot(), now delas with
-"scan.gwaa" and "scan.gwaa.2D" objects
-
-as.data.frame.gwaa.data which takes out @phdata part is arranged
-
-Fixed bug which made qtscore, ccfast and emp.* use phenotypes from
-the attached data frame, even when the data argument was supplied.
-For qtscore and emp.qtscore Formula now can be formulated as character
-and a formula.
-
-hom() function developed (previously heteroz; now is implemented in C)
-
-perid.summary() designed to produce average heterozygosity and call rate
-per person; this implied changes in check.marker() and summary.check.marker()
-
-ibs() function developed, this one extends to check.marker()
-
-A family of descriptives.* functions added: .marker, .trait, .scan
-
-Much improved genetic data QC (check.marker); new function Xfix()
-
-***** v 1.1-6 (2007.02.12)
-
-Improved memory managmenet. In particular, @chromosome slot is now
-stored as a factor.
-
-***** v 1.1-4 (2006.12.21)
-
-Due to accumulated changes, version number updated.
-
-Multiple improvements and fixes + catable() function
-
-***** v 1.1.3 (2006.11.12)
-
-scan.glm.2D and scan.haplo.2D functions added
-
-run.haplo.score.slide renamed to scan.haplo for consistency
-
-heteroz() added
-
-scan.gwaa-class is modified: effects are also returned.
-This led to modification of C code for fastcc, qtscore, R
-code for qtscore(), ccfast(), fcc(), emp.qtscore(), emp.ccfast(),
-scan.glm()
-
-improved memory management in functions ccfats(), emp.ccfast(),
-qtscore(), emp.qtscore(), summary()
-
-show.ncbi() added
-
-***** v 1.1.2
-
-scan.glm patched (it did not work with df=2 when a SNP had only 2 genotypes)
-
-minor fix in sub-setting of snp.data class
-
-ccfast, qtscore, scan.glm, emp.ccfast, emp.qtscore and plot.scan.gwaa are modified.
-Major change concerns ccfast and qtscore: now, 1-df and 2-df tests are
-computed simultaneously within the C functions.
-The class "scan.gwaa" now contains both 1- and 2-df P-values.
-This also addresses the point on TODO:
-
-2006.08.17 implement qtscore function with 2df
-
-Small fix in qtscore and ccfast (to act on 1 d.f. when # genotypic classes is 2)
-
-The function scan.gwaa removed as redundant
-
-qtscore now allows for analysis using strata (Cochran-Mantel-Haenszel)
-
-Added average/median chi2 to the "scan.gwaa" class (to be used for genomic
-control)
-
-TODO fixed:
-2006.10.11 q-value returned by qvaluebh95() is wrong
-
-emp.qtscore and emp.qtfast optimised (runs 3-10 times faster) by
-removing unnecessary checks and calling C function directly
-(instead of calling ccfast/qtscore)
-
-NAMESPACE introduced
-
-Update of documentation: now R CMD check passes all checks
-
-Formal class introduced for scan.gwaa-class
-
-demo(srdta): demo(srdtawin) is made by removing load-data from demo(srdta)
-because this may not work when there are no administrator's priviliges
-
-last modified 08.11.2006
-
-***** v 1.0.2
-
-Function scan.glm is introduced; this allows to scan for interactions in
-an easy way. This is essentially a modified scan.gwaa.
-
-New function to convert ped-files type of data to internal format,
-convert.snp.ped, was arranged
-
-Function add.plot.scan.gwaa was added
-
-Library "methods" loaded on start-up
-
-last modified 01.11.2006
-
-
-
-***** v. 1.0.1
-
-is resolving the issue of
-
-2006.07.20 need fast exact test for HWE, along the lines of fastcc,
- as HWE.exact is too slow (Yurii)
-
-and
-
-2006.10.11 gwaa.data should be easily sub-settable -- now one
- needs to extract @gtdata and subset and @phdata and
- subset and then merge (also using base R things) (Yurii)
Copied: pkg/GenABEL/ChangeLog (from rev 1320, pkg/GenABEL/CHANGES.LOG)
===================================================================
--- pkg/GenABEL/ChangeLog (rev 0)
+++ pkg/GenABEL/ChangeLog 2013-08-27 19:24:17 UTC (rev 1321)
@@ -0,0 +1,972 @@
+*** v. 1.7-7
+
+(2013.08.27)
+Removed CRAN version checks following the request from B. Ripley,
+fixing other problems identified by --as-cran checks ("iterator"
+package changed from "DatABEL" to "GenABEL"; renaming CHANGES.LOG to
+ChangeLog), releasing this version on CRAN
+
+(2013.07.19)
+Added warning that *2databel's may not produce output in desired data type
+and fall onto float
+
+(2013.06.29)
+Changed the 'polygenic' nullification threshold to 1e-8
+
+Added references for Grammar+ transformation
+
+Allowed for user-specified output data type in '*2databel' functions
+
+Changed version number to 1.7-7
+
+(2013.06.06)
+Two new functions added: LiLog() and palinear2LiLog() for the
+estimation of logistic beta's from a linear regression. Thanks to
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 1321
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