performWilcoxonTest: Perform the Wilcoxon rank sum and signed rank tests on...

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

Description

The function performWilcoxonTest performs a Wilcoxon rank sum and signed rank test on the loading values. The null hypothesis is that the mean of ranks of the marker loadings is smaller or equal to the ranks of the non-marker loadings. The null hypothesis can be rejected with probability p (alternative hypothesis: loadings of markers are greater than the loadings of non-markers).

Usage

performWilcoxonTest(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 performWilcoxonTest takes as input a tibble (tbl) that stores the loading values in the column "value" and the information on marker/non-marker in the column "type".

Value

htest

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
values <- assay(tanzer2020)
markers <- readMarkers(type = "apoptosis")

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

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