In VoisinneG/InteRact: Analysis of affinity purification/tandem MS data

knitr::opts_chunk$set(echo = TRUE)

InteRact

Analysis of affinity purification/tandem MS data with R

• flexible : no strict input format
• publication-ready figures

More info on the website

Install

The package is available from github:

devtools::install_github("VoisinneG/InteRact")

A shiny based GUI can be accessed here

Use

library(InteRact)

Load example protein group dataset and run InteRact:

data("proteinGroups_Cbl")
names(proteinGroups_Cbl)[1:10]

res <- InteRact(proteinGroups_Cbl, bait_gene_name = "Cbl")

Identify specific interactors

res <- identify_interactors(res,
                            p_val_thresh = 0.001, 
                            fold_change_thresh = 3, 
                            n_success_min = 1, 
                            consecutive_success = TRUE)
print(res$interactor)

Show summary table

sum_tbl <- summary_table(res)
head(sum_tbl[, c("bait", "names", "max_fold_change" ,"max_stoichio", "is_interactor")])

VoisinneG/InteRact documentation built on May 17, 2022, 11:40 p.m.