README.md

In twesleyb/SwipProteomics: Analysis of Swip TMT Spatial Proteomics

SwipProteomics

This repository is an archive of the proteomics data and source code used in the analyses by Courtland et al., 2021.

Please see soderling-lab/SwipProteomics for an extant version of this code.

Usage Example

# download the repository as an R package
devtools::install_github("twesleyb/SwipProteomics")

library(dplyr)
library(SwipProteomics)

# load the normalized data
data(swip_tmt)

# washc4's uniprot ID
data(swip)

# fit a model
fx <- log2(Intensity) ~ 0 + Condition + (1|Mixture)
fm <- lmerTest::lmer(fx,data=swip_tmt %>% subset(Protein==swip))

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

# assess contrast 
res <- lmerTestContrast(fm, LT) %>% mutate(Contrast='Mutant-Control') %>% unique()

knitr::kable(res)

|Contrast | log2FC| percentControl| SE| Tstatistic| Pvalue| DF| S2|isSingular | |:--------------|---------:|--------------:|---------:|----------:|------:|--:|--------:|:----------| |Mutant-Control | -1.401866| 0.3784393| 0.0264791| -52.94235| 0| 28| 0.007362|TRUE |

lmerTestContrast returns a data.frame with statistics from the model-based contrast. The column isSingular=TRUE in this case indicates that the variance attributes to Mixture is negligible.

## fit WASH Complex

library(dplyr)
library(SwipProteomics)

data(washc_prots)

# module-level model includes ranef Protein
fx1 <- log2(rel_Intensity) ~ 0 + Condition + (1|Protein)

# fit the model
fm1 <- lmerTest::lmer(fx1, data = swip_tmt %>% subset(Protein %in% washc_prots))

# assess overall 'Mutant-Control' comparison
res1 <- lmerTestContrast(fm1, LT) %>% mutate(Contrast='Mutant-Control') %>% unique()

knitr::kable(res)

|Contrast | log2FC| percentControl| SE| Tstatistic| Pvalue| DF| S2|isSingular | |:--------------|---------:|--------------:|---------:|----------:|------:|---:|---------:|:----------| |Mutant-Control | -1.379633| 0.3843165| 0.0392109| -35.18497| 0| 151| 0.0645747|FALSE |

twesleyb/SwipProteomics documentation built on Sept. 15, 2021, 7:38 a.m.