Make sure package devtools is installed.

To install MSnSet.utils run

devtools::install_github("PNNL-Comp-Mass-Spec/MSnSet.utils")

By default install_github does not compile vignettes. Thus to compile with vignettes use the following options.

devtools::install_github("PNNL-Comp-Mass-Spec/MSnSet.utils", build_vignettes = TRUE)

This is a collection of misc custom functions. They are primarily geared towards proteomics/perhaps-other-omics data analysis using MSnSet or ExpressionSet as data containers.

• heatmaps
• colorschemes
• nested linear models
• wrappers for the machine learning routines
• custom imputation
• reading of MaxQuant and SkyLine data
• handling PTM mapping
• PCA plots
• volcano plots
• wrappers for LIMMA differential analysis pipelines

The orignal location is on the vladpetyuk account, repo vp.misc.