Section 1 Introduction

This is the complete markdown workflow of the code referring to Di Fraia et al.

1.1 About the built-in packages

This docker container comes with 3 in house produced R packages that contains useful functions for working with this kind of data. The proteomicstools packages contains useful functions for manipulating proteomics data matrix, plotting purposes and contains useful functions for dealing with protein complexes. The paralogstools packages functions are used to more easily work with Paralog genes. The spatialR package is a very broad and unspecific packages, used by the author to manipulate various data sources and types. It contains lots of different function for working with different kind of data structures. During this workflow is mainly used to running GOEnrichment analysis. Lots of these packages are layed out using other packages, expecially the ones coming from the BioconductoR consortium.

The majority of functions present in each of the packages is documented as much as possible.

1.2 Getting Started

To correctly link the file path to this documentation please set your working directory inside the Markdown folders.

setwd('Markdown')

You can either work following and running again the .Rmd files present inside the Markdown folder, or alternatively run your independent R session to explore the data by yourself, just referring at the complete markdown for some reference.