CHANGES IN VERSION 1.18.3 Bug fixes -------------------------- o fix issue with residuals() where examples fail o fix issues with residuals() - https://github.com/GabrielHoffman/variancePartition/issues/18 o fix issue exporting eBayes, topTable, etc o Improve documentation for contrasts in dream.Rmd o check that contrasts sum to zero in plotContrasts. o in voomWithDreamWeights() fix issue with not defining design - https://github.com/GabrielHoffman/variancePartition/issues/17 o in voomWithDreamWeights() fix issue with returning design matrix o better error if counts can't be converted to matrix - https://github.com/GabrielHoffman/variancePartition/issues/15 o Round numbers in plotContrasts() o fix issues with strings are passed to formula arguments CHANGES IN VERSION 1.18.2 Bug fixes ------------------------- o New gives meaning full error message for dream(), etc when variable is not found in data. o Better error catching when running fitVarPartModel() with fxn that fails o add get_prediction() function - the following code now can be run in parallel fitList = fitVarPartModel( Y, ~ (1|Batch), data, fxn = function(fit){ B = variancePartition::get_prediction(fit, ~(1|Batch)) fit@resp$y - B }, BPPARAM=SnowParam(3)) o Update vignette #3, and update documentation of REML argument o add new FAQ.Rmd o canCorPairs() now returns NA correlation when two variables have no overlapping observed values o plotCorrMatrix() now handles NA correlation values o Improve documentation o move location of eBayesFMT code o Clean up some code and add documentation o document ebayesFMT o Clean up some code and add documentation o compute effective degrees of freedom for each model CHANGES IN VERSION 1.18.0 ------------------------- o Bioconductor freeze CHANGES IN VERSION 1.17.10 ------------------------- o fix issue returning residuals from limma CHANGES IN VERSION 1.17.10 ------------------------- o resolve issue where dream gives error: r[cbind(1L:p, 1L:p)] <- 1 : subscript out of bounds - only occured when no fixed effects were used CHANGES IN VERSION 1.17.9 ------------------------- o Fix issues with compatability with R/4.0.0 CHANGES IN VERSION 1.17.8 ------------------------- o Better error message when response contains missing data CHANGES IN VERSION 1.17.7 ------------------------- o Better error message when variable in formula does not exist CHANGES IN VERSION 1.17.6 ------------------------- o comply with new Bioconductor check: _R_CHECK_LENGTH_1_LOGIC2_ CHANGES IN VERSION 1.17.5 ------------------------- o if contrasts for dream() is data.frame, convert to matrix CHANGES IN VERSION 1.17.4 ------------------------- o Don't print warnings for residuals() when only one argument passed. o fix bug with residuals evaluated with only fixed effects CHANGES IN VERSION 1.17.3 ------------------------- o Allow sparseMatrix for gene expression. Now saves memory by avoiding conversion to matrix. Processing sparseMatrix will be slower, but memory usage will be low. o dream(..., computeResiduals=TRUE) now computes residuals and allows use of residuals() function CHANGES IN VERSION 1.17.2 ------------------------- o fix error in voomWithDreamWeights() when design matrix is null CHANGES IN VERSION 1.17.1 ------------------------- o topTable(...,sort.by=) now is correct when and F-test is used o fixed issue in classifyTestsF.MArrayLM2, now is much faster CHANGES IN VERSION 1.15.8 ------------------------- o Replace cat() with message() o add quiet option to a few functions o dream() does not call eBayes() when lmFit is used CHANGES IN VERSION 1.15.7 ------------------------- o Official release to development branch CHANGES IN VERSION 1.15.6 ------------------------- o fix convergence errror when recycling parameters values from first gene o add column z.std and F.std to topTable CHANGES IN VERSION 1.15.4 ------------------------- o Add error message when scale of fixed effects causes a problem CHANGES IN VERSION 1.15.3 ------------------------- o Try changing order of eBayes CHANGES IN VERSION 1.15.2 ------------------------- o Update vignette CHANGES IN VERSION 1.15.0 ------------------------- o Push changes to Bioconductor devel CHANGES IN VERSION 1.13.11 ------------------------- o Fixed bug in voomWithDreamWeights() with approxfun() with ties CHANGES IN VERSION 1.13.10 ------------------------- o fix parallel processing issues CHANGES IN VERSION 1.13.9 ------------------------- o update vignette for new parallel processing backend CHANGES IN VERSION 1.13.8 ------------------------- o apply empirical Bayes when doing F-test o hypothesis testing for single coefficients is now included by default, so only need to specify contrast matrix if for more complicated contrasts o add voomWithDreamWeights() for computing observation weights using random effects o Add BiocParallel capability with BPPARAM argument - allows parallel processing with lower memory usage o dream() is now compatable with gene set enrichments from pinnacle (software comming soon) CHANGES IN VERSION 1.13.7 ------------------------- o in dream(), add support for genes annotation in DGElist() o in dream(), automatically evaluate contrasts for all single coefficients o add future compatability for gene set enrichments method "pinnacle" CHANGES IN VERSION 1.13.5 ------------------------- o add plotContrasts() to dream vignette CHANGES IN VERSION 1.13.4 ------------------------- o export classes to fix bug with class "varPartResults" not being defined o Thanks Megan Behringer CHANGES IN VERSION 1.13.3 ------------------------- o add plotContrasts() CHANGES IN VERSION 1.13.2 ------------------------- o Enable random slope models in dream, but not for estimating variance fractions o Thanks Jonas Zierer CHANGES IN VERSION 1.13.1 ------------------------- o Add progress bar at ETA ======= CHANGES IN VERSION 1.12.4 ------------------------- o Update dream vignette CHANGES IN VERSION 1.12.3 ------------------------- o add plotContrasts() o Enable random slope models in dream, but not for estimating variance fractions o export classes to fix bug with class "varPartResults" not being defined - Thanks Megan Behringer CHANGES IN VERSION 1.11.13 ------------------------- o Fix multithreading issue CHANGES IN VERSION 1.11.11 ------------------------- o dream can handle multiple contrasts at the same time CHANGES IN VERSION 1.11.10 ------------------------- o fix typos in dream vignette CHANGES IN VERSION 1.11.8 ------------------------- o Check and stop() if response variable has variance of 0 - in dream(), fitExtractVarPartModel(), and fitVarPartModel() o add standardized_t_stat() implicitly in eBayes() using MArrayLM2 class - this transforms moderated t-statistics to have same degrees of freedom CHANGES IN VERSION 1.11.7 ------------------------- o Simplify object return by dream to be more more similar to lmFit - now returns MArrayLM instead of MArrayLMM_lmer o if a fixed effects formula is specified (i.e. not random terms) - dream call lmFit in the backend - getContrast() works seamlessly o dream() now returns gene annotation if passed to function CHANGES IN VERSION 1.11.6 ------------------------- o add error checing for L in dream o fix typoes in dream vignette o fix typoes in theory_practice_random_effects.Rnw CHANGES IN VERSION 1.11.5 ------------------------- o Add dream function for differential expression for repeated measures with a linear mixed model CHANGES IN VERSION 1.11.2 ------------------------- o Add warnings to canCorPairs for colinear terms CHANGES IN VERSION 1.11.1 ------------------------- o Add vignette: theory_practice_random_effects.Rnw CHANGES IN VERSION 1.9.9 ------------------------- o Fix issue when package is autoloaded when starting R CHANGES IN VERSION 1.9.8 ------------------------- o Fix issue where if info data.frame contained a column name "gene", fitExtractVarPartModel() would not run CHANGES IN VERSION 1.9.6 ------------------------- o Fix tximport issue with eval=FALSE CHANGES IN VERSION 1.9.2 ------------------------- o Fix vignette CHANGES IN VERSION 1.9.1 ------------------------- o Fix formatting of vignette o add description of canCorPairs() function CHANGES IN VERSION 1.5.7 ------------------------- o include splines in foreach .packages CHANGES IN VERSION 1.5.6 ------------------------- o compatibility with tximport v1.3.5 CHANGES IN VERSION 1.5.5 ------------------------- o Decrease computing time of effective sample size with ESS() by additional ~10x with sparse solver o fix margins for plotPercentBars() o Fix bug for getVarianceComponents() when correlated continous variables are included o compatibility with ggplot2 2.2.0 o center plot titles o fix order of bars in plotPercentBars() o legend background to transparent o set text to be black o include lme4 in foreach .packages o change residuals color to not be transparent o add CITATION information o plotCorrMatrix now shows dendrogram by default o Estimate run time for fitExtractVarPartModel() / fitVarPartModel() o improve warnings for plotPercentBar() o improve warnings for plotCorrStructure() o define ylab for plotVarPart() - add as.matrix.varPartResults() (hidden) - define isVaryingCoefficientModel() (hidden) CHANGES IN VERSION 1.3.11 ------------------------- o in canCorPairs() and other functions, convert formula with as.formula() o improve error messages for canCorPairs() CHANGES IN VERSION 1.3.10 ------------------------- o Add plotStratify() o Update documentation CHANGES IN VERSION 1.3.8 ------------------------- o Add additional examples to vignette o show projected memory usage of fitVarPartModel() CHANGES IN VERSION 1.3.7 ------------------------- o fitVarPartModel warns if names in exprObj and data are not identical o residuals() and other functions deal with missing values properly CHANGES IN VERSION 1.3.6 ------------------------- o Small changes to vignette CHANGES IN VERSION 1.3.5 ------------------------- o Fix Bioconductor error CHANGES IN VERSION 1.3.4 ------------------------- o Fix typos CHANGES IN VERSION 1.3.3 ------------------------- o Improve documentation CHANGES IN VERSION 1.1.9 ------------------------- o Update sortCols to handle Measurement.error o change backend package structure o set Residuals to be grey by default in plotVarPart() and plotPercentBars() o add control = lme4::lmerControl(calc.derivs=FALSE, check.rankX="stop.deficient" ) o add plotCorrStructure CHANGES IN VERSION 1.1.8 ------------------------- o Add ESS.R o Add fitVarTest.R o use lmerTest by default o fix bug checkModelStatus() for variables with backticks in name CHANGES IN VERSION 1.1.7 ------------------------- o GPL License CHANGES IN VERSION 1.1.6 ------------------------- o Move packages from Depends to Imports o For clarity, replace = with <- in parts of examples and vignette o Stop cluster in examples to solve error on Windows machines CHANGES IN VERSION 1.1.5 ------------------------- o Stop cluster in vignette to solve error on Windows machines CHANGES IN VERSION 1.1.4 ------------------------- o Fix Bioconductor check error CHANGES IN VERSION 1.1.3 ------------------------- o Add details to vignette o Fix ggplot2 compatibility issues CHANGES IN VERSION 1.1.2 ------------------------- o Add details to vignette CHANGES IN VERSION 1.1.1 ------------------------- o add plotPercentBars() to vizualize variance fractions for a subset of genes o add ESS() to compute effective sample size o fix x.labels argument in plotStratifyBy(). Previously, this argument was not used correctly CHANGES IN VERSION 1.0.0 ------------------------- o Release to Bioconductor 3.2 CHANGES IN VERSION 0.99.9 ------------------------- o add legend argument to plotStratifyBy() o improve warnings / errors for varying coefficient models o allow user to manually adjust cutoff for determining when design matrix is singular - changed default cutoff to 0.999 from 0.99 CHANGES IN VERSION 0.99.8 ------------------------- o improve warnings / errors when design matrix is close to or exactly singular CHANGES IN VERSION 0.99.7 ------------------------- o added new class varPartResults to store results of fitExtractVarPartModel() and extractVarPart() - the user will not notice any change, only the backend is different o Allow computation of adjusted ICC in addition to ICC. o add warning when categorical variables are modeled as fixed effects o fix computation of variance fractions for varying coefficient models o add getVarianceComponents() to return variances from lmer() or lm() model fit o showWarnings=FALSE suppresses warning messages o add fxn argument to fitVarPartModel to evaluate any function on the model fit CHANGES IN VERSION 0.99.6 ------------------------- o Update DESCRIPTION information CHANGES IN VERSION 0.99.5 ------------------------- o residuals deals with missing data gracefully and returns a matrix CHANGES IN VERSION 0.99.4 ------------------------- o add documentation for example datasets o convert calcVarPart() to S4 from S3 function call o fix typos in vignette CHANGES IN VERSION 0.99.3 ------------------------- o fitVarPartModel() and fitExractVarPartModel() use S4 instead of S3 calls CHANGES IN VERSION 0.99.2 ------------------------- o rename sort.varParFrac to sortCols o support ExpressionSet o change options for plotStratifyBy() # Before Bioconductor submission CHANGES IN VERSION 0.0.12 ------------------------- o add plotStratifyBy() o update documentation CHANGES IN VERSION 0.0.11 ------------------------- o fix sort to work on correct argument CHANGES IN VERSION 0.0.10 ------------------------- o fitExtractVarPartModel() and fitVarPartModel() now take subset argument o throw warning when no Intercept is specified o if using lmer, warning if categorical variable is modeled as fixed effect o fixed calcVarPart bug with reporting too few variances for multicategory fixed effects o add colinearityScore CHANGES IN VERSION 0.0.9 ------------------------- o function now use the precision weights when specified o remove warning about unspecified weights, when useWeights=TRUE o fix issue with sort with only one variable o add main argument to plotVarPart CHANGES IN VERSION 0.0.8 ------------------------- o Bug update to vignette and simulated data CHANGES IN VERSION 0.0.7 ------------------------- o remove 'variable' from xlab of plotVarPart CHANGES IN VERSION 0.0.6 ------------------------- o set REML=FALSE to default. This fixes issues of inaccurate variance estiamtes, and makes lmer() results more concordant with lm() results o Fix residuals function when lm or lmer is used o fix useWeights argument error for fitExtractVarPartModel() CHANGES IN VERSION 0.0.5 ------------------------- o plotVarPart() as ylim=c(0,100) as default, and can be changed by user o fitExtractVarPartModel() labels rows correctly CHANGES IN VERSION 0.0.4 ------------------------- o Add sort() for output of extractVarPart() or fitExtractVarPartModel() CHANGES IN VERSION 0.0.3 ------------------------- o add residuals function o add fitExtractVarPartModel() o foreach loops us iterators CHANGES IN VERSION 0.99.0 ------------------------- o Initial version