Bioconductor Code: ExploreModelMatrix (original) (raw)

# ExploreModelMatrix [\](https://codecov.io/github/csoneson/ExploreModelMatrix) [\](https://github.com/csoneson/ExploreModelMatrix/actions) `ExploreModelMatrix` is a small R package that lets the user interactively explore a design matrix as generated by the `model.matrix()` R function. In particular, given a table with sample information and a design formula, `ExploreModelMatrix` illustrates the fitted values from a general linear model (or, more generally, the value of the linear predictor of a generalized linear model) for each combination of input variables, simplifying understanding and generation of contrasts. A number of other visualizations are also included in the interactive interface, particularly simplifying the interpretation of linear models.  ## Installation You can install `ExploreModelMatrix` from Bioconductor (note that you need at least release 3.11 of Bioconductor, released in April 2020): ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("ExploreModelMatrix") ``` ## Usage The main function in the `ExploreModelMatrix` package is called `ExploreModelMatrix()`. When calling `ExploreModelMatrix()`, simply provide a _data.frame_ (or _DataFrame_) with sample information and a design formula: ``` sampleData <- data.frame(genotype = rep(c("A", "B"), each = 4), treatment = rep(c("ctrl", "trt"), 4)) ExploreModelMatrix(sampleData = sampleData, designFormula = ~ genotype + treatment) ``` This will open up an [R/Shiny](https://shiny.rstudio.com/) application where you can explore the specified design matrix and the fitted values for each combination of predictor values. For more examples of designs, we refer to the package vignette.