gs_to_sce: Convert GatingSet to SCE with option to run UMAP as well

In NKInstinct/flowHelpers: Personal Helper Functions for Cytometry Analysis

Convert GatingSet to SCE with option to run UMAP as well

Description

This function is very similar to gs_to_Seurat, but rather than shoehorning all the flow data into Seurat's structures, it falls back to using just (tidy)SingleCellExperiment packages and constructors.

Usage

gs_to_sce(
  gs,
  node = "root",
  condition = Biobase::sampleNames(gs),
  do_UMAP = FALSE,
  feature_exclusion = NULL
)

Arguments

gs	The GatingSet to draw the data from
node	A string specifying which gate to take data from. Defaults to "root" (all acquired events)
condition	A vector of strings specifying which group each sample belongs to. Must be of the same length as the number of samples in gs, and must be in the same order as the samples in gs (can check this with sampleNames(gs)). Defaults to just the sampleNames themselves, which is not ideal so you should probably specify something here!
do_UMAP	A boolean specifying whether to run UMAP dimensional reduction or not. This is the whole point of turning flow data into an SCE, but it can be computationally intense for even moderately sized experiments so you need to opt-in.
feature_exclusion	A regular expression specifying which rownames to exclude from building the UMAP. Defaults to NULL (no exclusions), but you likely want to exclude Time, FSC/SSC, and Viability at least since these should be pre-gated.

Details

Note that if you want to be able to interact with the sce in tidy format, you should attach tidySingleCellExperiment yourself!

NKInstinct/flowHelpers documentation built on March 17, 2023, 1:42 a.m.