prepareTbl: Helper function to create the output of createLoadingsTbl

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

Description

The function prepareTbl prepares the input for createLoadingsTbl using the intensity values (values) and the tibble with markers (markers).

Usage

prepareTbl(values, markers, PC = "PC1")

Arguments

values	matrix or data.frame
markers	tbl
PC	character, has to be in the format "PC1", "PC2", "PC3", ..., the specification of multiple principal components is possible and the length of loadings vectors will be calculated using these principal components

Details

The function will call internally the helper function combineLoadings. This means the function will return absolute loadings values even in the case of only one selected principal component.

Examples

library(MatrixQCvis)
library(SummarizedExperiment)

## load data set of Tanzer et al. (2020)
## source: https://www.ebi.ac.uk/pride/archive/projects/PXD014966
f <- system.file("protein_datasets/tanzer2020.RDS", 
    package = "apoptosisQuantification")
tanzer2020 <- readRDS(f)

## get loadings of markers and of the complete data set
prot <- assay(tanzer2020)
markers <- readMarkers(type = "apoptosis")

apoptosisQuantification:::prepareTbl(values = prot, markers = markers, 
    PC = "PC1")

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