In VoisinneG/proteinRuler: proteinRuler

library(knitr)
knitr::opts_chunk$set(echo = TRUE, message=FALSE, warnings=FALSE)
devtools::load_all()

R Package : proteinRuler

Compute protein abundance from protein intensities using the 'protein ruler' methodology (See article by Wisniewski et. al).

Install

Install the package from github using devtools:

devtools::install_github("VoisinneG/proteinRuler")
library(proteinRuler)

Examples

Import a dataset containing protein intensities and protein IDs and compute protein abundances :

data("proteinGroups_CD4_Tcells")
res <- proteinRuler(proteinGroups_CD4_Tcells, DNA_mass_per_cell = 5.5209e-12, show_progress = FALSE)
names(res)
print(res$summary)

Plot copy number distribution :

cond <- "CopyNumber_WT_0"
hist(log10(res$copy_number[[cond]]), main = "", xlab = paste(cond, "(log10)"), col = rgb(1,0,0,0.25))

VoisinneG/proteinRuler documentation built on Oct. 13, 2022, 9:47 p.m.