NEWS.md

In glmmSeq: General Linear Mixed Models for Gene-Level Differential Expression

News

glmmSeq v0.5.5

29/09/2022

• Improve error handling if all genes give errors

glmmSeq v0.5.4

25/09/2022

• Add option for likelihood ratio test (LRT) in glmmSeq() and lmmSeq()
• Enable changing of model formula, family and control parameters when refitting model for a single gene in glmmRefit()

glmmSeq v0.5.2

19/09/2022

• Fix passing of ... in parallelisation on windows in glmmSeq() & lmmSeq()

glmmSeq v0.5.1

02/09/2022

• Add option to glmmSeq() to use glmmTMB package for fitting negative binomial GLMM (or other GLM family) models
• Add plab argument to modelPlots to customise p-value labels
• Add mean expression column meanExp to results in @stats$res slot

glmmSeq v0.4.0

10/08/2022

• Further speed enhancements to lmmSeq() using lme4::modular code. Speed increase of around 25%.

glmmSeq v0.3.0

05/08/2022

• Significant update including output of standard error on fitted coefficients for both glmmSeq and lmmSeq
• Add summary function for glmmSeq and lmmSeq to display results for an individual gene
• Reorganised @stats slot 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 lmmSeq using the lmerTest package
• Added lmmRefit function to fit an identical (g)lmer model. This can then be passed to the emmeans package for visualisation of more complex models.
• Separated modelPlots (base graphics) and ggmodelPlots (ggplot2)
• Streamlined modelPlots to allow for simplest case gene ~ Time + (1 | ID)

glmmSeq v0.2.2

16/07/2022

• 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 id column name from the RE term in the formula

glmmSeq v0.2.1

11/07/2022

• Add ... option to fcPlot which is passed to plotly() or ggplot()
• set annotationPosition=FALSE in fcPlot so arrows/connectors are not moved

glmmSeq v0.2.0

09/07/2022

• Add lmmSeq function for gaussian linear mixed models

glmmSeq v0.1.2

08/07/2022

• Fix CMD check errors

glmmSeq v0.1.1

18/04/2021

Bug Fixes

• Fix colours in pairedPlots and modelPlots

glmmSeq v0.1.0

16/03/2021

Features

• Add progress bars to glmmSeq functions
• Add option returnList to return glmmSeq output as list (to make error catching easier)

Bug Fixes

• Fix missing plots in vignette

glmmSeq v0.0.1

05/03/2021

• This is the initial build of glmmSeq

glmmSeq documentation built on Oct. 8, 2022, 5:05 p.m.