divideByReference: Divide assay columns by a reference column

In UCLouvain-CBIO/scp: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Divide assay columns by a reference column

Description

The function divides the sample columns by a reference column. The sample and reference columns are defined based on the provided colvar variable and on regular expression matching.

Usage

divideByReference(object, i, colvar, samplePattern = ".", refPattern)

Arguments

object	A QFeatures object
i	A numeric() or character() vector indicating from which assays the rowData should be taken.
colvar	A character(1) indicating the variable to take from colData(object) that gives the sample annotation.
samplePattern	A character(1) pattern that matches the sample encoding in colvar. By default all samples are devided (using the regex wildcard .).
refPattern	A character(1) pattern that matches the carrier encoding in colvar. Only one match per assay is allowed, otherwise only the first match is taken

Details

The supplied assay(s) are replaced with the values computed after reference division.

Value

A QFeatures object

Examples

data("scp1")
scp1 <- divideByReference(scp1, 
                          i = 1, 
                          colvar = "SampleType",
                          samplePattern = "Macrophage",
                          refPattern = "Ref")
                          

UCLouvain-CBIO/scp documentation built on May 5, 2024, 1:17 a.m.