In soderling-lab/tidyProt: tidy statistical analysis of protein mass spectrometry

Demo

knitr::opts_chunk$set(echo = TRUE, out.width="100%")

# imports

library(dplyr)
library(tidyProt) # soderling-lab/tidyProt

# load the iPSD BioID data

# devtools::install_github("soderling-lab/Uezu")
data(ipsd_bioid, package="Uezu2016") 


# fit a simple linear model
fx <- log2(Intensity) ~ 0 + Condition
fm <- lm(fx, ipsd_bioid %>% subset(Symbol == "Gphn"))

# create a contrast for Gephyrin BioID versus control
LT <- getContrast(fm,"Gephyrin","ConditionControl")

# assess contrast
lmTestContrast(fm, LT) %>% knitr::kable()

soderling-lab/tidyProt documentation built on Dec. 23, 2021, 3:31 a.m.