README.md

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

tidyProt

Installation

To install the tidyProt package, type the following into an R console: devtools::install_github("soderling-lab/tidyProt").

Key Dependencies

Before installing tidyProt, insure that you have installed the following R packages:

• lmerTest install.packages("lmerTest")
• dplyr install.packages("dplyr")
• data.table install.packages("data.table")
• reshape2 install.packages("reshape2")

Usage

# work with data from soderling-lab/SwipProteomics
# devtools::install_github("soderling-lab/SwipProteomics")

library(dplyr)
library(tidyProt)

library(SwipProteomics)  

data(washc) # wash complex proteins
data(wash_bioid) # the normalized proximity proteomics data

## linear model-based comparison
fx <- log2(Intensity) ~ 0 + Condition
fm <- lm(fx, data=wash_bioid %>% subset(Accession==washc[1]))

fm

# create a contrast
LT <- getContrast(fm, "WASH","Control")

# assess comparison
lmTestContrast(fm, LT)

## linear mixed-model based comparison
data(swip_tmt)

fx <- log2(rel_Intensity) ~ 0 + Condition + (1|Protein)

fm <- lmerTest::lmer(fx, data = swip_tmt %>% subset(Protein %in% washc))

LT <- getContrast(fm, "Mutant", "Control")

lmerTestContrast(fm, LT)

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