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MSnSet.utils

R-CMD-check

Installation

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)

Description

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

Original Location

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