decoupleFeatures: Calculate score values using decoupleR/run_wmean

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

Description

The function decoupleFeatures calculates contamination scores using the run_wmean function from the decoupleR. The function will return score values (per sample) that can be interpreted as the standard deviations away from an empirical null distribution.

Usage

decoupleFeatures(
  values,
  args_fct,
  contamination = c("apoptosis", "necroptosis")
)

Arguments

values	matrix, the rownames contain the feature names (SYMBOL ids) and colnames the samples
args_fct	list, containing the entries "n_perm" (numeric(1) and "signatures" (tibble)
contamination	character(1), either "apoptosis" or "necroptosis"

Details

The function is insprired by the work of Aurelien Dugourd and his plasmaContamination package (https://github.com/saezlab/plasmaContamination/).

The function will be called in scoreSamples.

Value

tibble

Examples

library(SummarizedExperiment)
f <- system.file("protein_datasets/tanzer2020.RDS", 
    package = "apoptosisQuantification")
tanzer2020 <- readRDS(f)
prot <- assay(tanzer2020) |>
    as.data.frame()

## define a list with paramters
args_fct <- list()
args_fct[["signatures"]] <- readMarkers(type = "apoptosis", fc = 2, n = 1)
args_fct[["n_perm"]] <- 100

## run the function
decoupleFeatures(values = prot, args_fct = args_fct, 
    contamination = "apoptosis")

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