getLoadingsOfMarkers: Get PCA loadings of marker features

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

Description

The function getLoadingsOfMarkers retrieves the loadings of the marker features (defined by markers) of the values data set.

getLoadingsOfMarkers returns a tibble of the marker features found in values containing the loadings for the principal components.

Usage

getLoadingsOfMarkers(values, markers)

Arguments

values	matrix or data.frame
markers	tbl

Details

In case there are ambiguous/multiple assignments of features (containing markers) to a loading value (MaxQuant separates these assignments by ";"), the features that are not in markers$feature are removed. In case there are multiple assignments left of marker features, the mean value of the loading values are returned.

Value

tibble

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(MatrixQCvis)
library(SummarizedExperiment)

## "apoptosis"
markers <- readMarkers(type = "apoptosis")
f <- system.file("protein_datasets/tanzer2020.RDS", 
    package = "apoptosisQuantification")
se <- readRDS(f)
prot <- assay(se) |>
    imputeAssay(method = "MinDet")
apoptosisQuantification:::getLoadingsOfMarkers(values = prot, 
    markers = markers)

## "nectroptosis"
markers <- readMarkers(type = "necroptosis")
apoptosisQuantification:::getLoadingsOfMarkers(values = prot, 
    markers = markers)

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