select_backbone_and_exploratory_markers: For each parameter in the FCS files, interactively prompts...

In ebecht/infinityFlow: Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions

For each parameter in the FCS files, interactively prompts whether it is part of the Backbone, the Infinity (exploratory) markers or should be ignored.

Description

This function will load the first of the input FCS files and extract the measured parameters as well as their labels. For each of these, it will ask the user whether it is part of the backbone measurements (which will be used as a predictor variable in regressions models), Infinity (exploratory) measurements (usually PE-conjugated or APC-conjugated, used as dependent/target variable in regressions) or discarded (e.g. for parameter such as Time, Sample IDs, Event number IDs, ...).

Usage

select_backbone_and_exploratory_markers(files)

Arguments

files

character vector of paths to FCS files

Value

A data.frame

Examples

data(steady_state_lung)
dir  <-  tempdir()
fcs_tmp  <-  file.path(dir, "tmp.fcs")
library(flowCore)
write.FCS(steady_state_lung[[1]], file  <-  fcs_tmp)
if(interactive()){
    select_backbone_and_exploratory_markers(fcs_tmp)
}

ebecht/infinityFlow documentation built on Jan. 31, 2024, 11:31 p.m.