scoreSamples: scoreSamples

In tnaake/apoptosisQuantification: Assessment of apoptosis and necroptosus unsing proteomics

Description

This function performs an enrichment analysis to test whether a given proteomic sample is contaminated with markers from apoptosis or necroptosis.

Usage

scoreSamples(values, contamination = c("apoptosis", "necroptosis"), ...)

Arguments

values	numeric vector, matrix, or data.frame
contamination	character(1), either "apoptosis" or "necroptosis"
...	further arguments passed to readMarkers

Details

The parameter values has to have (gene) symbols as row.names. values can be either a numeric vector, matrix, or data.frame. It holds the normalized intensity values of features (e.g. proteins).

The signatures are taken per default from Tanzer et al. (2020), but also a tibble containing the contamination markers can be given to the function as argument signatures. In that case the tibble has to contain at least the column "feature" that contains the marker features (e.g. proteins).

The function will either run decoupleFeatures or permuteFeatures to calculate scores. The behaviour will be triggered by the presence of the column value in signatures (in that case, decoupleFeatures is run).

Value

data.frame, containining normalized enrichment (mean) scores for the contamination signature (the higher the score, the higher the potential contamination). If there is no quantitative information on changes (e.g. fold changes or t-values), the function will return an empirical distribution of difference of means of the markers to all features in the data set

References

Tanzer et al. (2020): Quantitative and Dynamic Catalogs of Proteins Released during Apoptotic and Necroptotic Cell Death. Cell Reports, 30, 1260-1270.e5. 10.1016/j.celrep.2019.12.079.

Examples

library(SummarizedExperiment)

f <- system.file("protein_datasets/tanzer2020.RDS", 
    package = "apoptosisQuantification")
tanzer2020 <- readRDS(f)
prot <- assay(tanzer2020)

## use the intensities to calculate scores, the function will load the 
## data set of Tanzer et al. (2020)
scoreSamples(values = prot, contamination = "apoptosis", n_perm = 100)

## use the contamination scores of Tanzer et al. (2020), but with specified
## fc and n_significan

tnaake/apoptosisQuantification documentation built on Feb. 20, 2022, 5:37 p.m.