In amkeele2/DukeProteomicsSuite: Pipeline for Proteomic Energetic Methods

knitr::opts_chunk$set(collapse = T, comment = "#>")
options(tibble.print_min = 4L, tibble.print_max = 4L)
set.seed(1000)

library(DukeProteomicsSuite)

This vignette introduces DukeProteomicsSuite functions and helps those unfamiliar with energetic proteomics methods to better understand what this package does and how it can be used. We'll start with a rough overview of energetic proteomics methods, then discuss where this package can be used, and finally provide real-world examples.

Overview

Proteomics is a broad field of

Talk about expression level vs phenotype analysis

OnePotTPP

TPP can be accessed using OnePotTPP_Phenotype.Fun() or OnePotTPP_Ligand.Fun() Can introduce error messages if p value is out of range or a TMTPlex is selected which is not currently available

OnePotTPP_Ligand.Fun(TPPExample_Ligand, p_cutoff = -5)

OnePotTPP_Ligand.Fun(TPPExample_Ligand, TMTplex = 8)

Look at example data by ?TPPExample_Ligand

OnePotTPP_Phenotype.Fun()

Calculates the Introduce the method Go through the analysis Examples

OnePotSPROX

Introduce the method Go through the analysis Examples

STEPP/LiP

Here we go knit

Here is some code

library(DukeProteomicsSuite)

amkeele2/DukeProteomicsSuite documentation built on April 27, 2021, 6:41 a.m.