This workshop is designed to work with RStudio Cloud. Go to https://rstudio.cloud/ (Monash users can log in with their Monash google account) and create a new project. The workshop can also be done using R locally on your laptop (if doing this, we also recommend you create a new project to contain the files).
Running the R code below will download files and install packages used in this workshop.
# Download data download.file( "https://monashdatafluency.github.io/r-linear/r-linear-files.zip", destfile="r-linear-files.zip") unzip("r-linear-files.zip") # Install some CRAN packages: install.packages(c( "tidyverse", "multcomp", "emmeans", "lme4", "lmerTest", "pbkrtest", "BiocManager")) # Install some Bioconductor packages: BiocManager::install(c("limma","edgeR","topconfects"))
Now load the file
linear_models.R in the
Built-in to R:
lm, model.matrix, coef, sigma, df.residual, predict, confint, summary, anova, drop1, I, poly
splines – curve fitting:
emmeans – linear hypothesis tests and multiple comparisons:
glht, mcp, confint, summary, emmeans
edgeR – fitting many models to gene expression data:
DGEList, calcNormFactors, cpm, lmFit, contrasts.fit, eBayes, plotSA, topTable