- Improve error handling if all genes give errors
- Add option for likelihood ratio test (LRT) in
glmmSeq()andlmmSeq() - Enable changing of model formula, family and control parameters when refitting
model for a single gene in
glmmRefit()
- Fix passing of
...in parallelisation on windows inglmmSeq()&lmmSeq()
- Add option to
glmmSeq()to useglmmTMBpackage for fitting negative binomial GLMM (or other GLM family) models - Add
plabargument tomodelPlotsto customise p-value labels - Add mean expression column
meanExpto results in@stats$resslot
- Further speed enhancements to
lmmSeq()usinglme4::modularcode. Speed increase of around 25%.
- Significant update including output of standard error on fitted coefficients
for both
glmmSeqandlmmSeq - Add
summaryfunction for glmmSeq and lmmSeq to display results for an individual gene - Reorganised
@statsslot in output objects to include more information including DF - Added option of using Saiterthwaite's DF method with ANOVA type III tables as
option for
lmmSequsing thelmerTestpackage - Added
lmmRefitfunction to fit an identical (g)lmer model. This can then be passed to theemmeanspackage for visualisation of more complex models. - Separated
modelPlots(base graphics) andggmodelPlots(ggplot2) - Streamlined
modelPlotsto allow for simplest casegene ~ Time + (1 | ID)
- Fast version of
lmmSeq(). Improves speed of calculation of type 2 Wald test. Overall speed increase of 25-50%. - Faster version of
glmmSeq() - Automatically detects
idcolumn name from the RE term in the formula
- Add
...option tofcPlotwhich is passed toplotly()orggplot() - set
annotationPosition=FALSEinfcPlotso arrows/connectors are not moved
- Add lmmSeq function for gaussian linear mixed models
- Fix CMD check errors
- Fix colours in pairedPlots and modelPlots
- Add progress bars to glmmSeq functions
- Add option
returnListto return glmmSeq output as list (to make error catching easier)
- Fix missing plots in vignette
- This is the initial build of
glmmSeq