dim.reduction: Calculate dimensional reductions

In jgarces02/FlowCT: A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets

Calculate dimensional reductions

Description

It calculates a dimensional reduction (DR) from a fcs.SCE object (or an expression table). Three different DR methods are available: Principal Component Analsis (PCA), t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP).

Usage

## S3 method for class 'reduction'
dim(
  data,
  assay.i = "normalized",
  markers.to.use = "all",
  dr.method,
  num.threads = NULL,
  perplexity.tsne = 100,
  n.neighbors.umap = 50
)

Arguments

data	A fcs.SCE object generated through FlowCT::fcs.SCE() or a expression table with events in rows and markers in columns.
assay.i	Name of matrix stored in the fcs.SCE object from which calculate the DR (this option is useless if input is not a fcs.SCE object). Default = "normalized".
markers.to.use	Markers to take account in the DR calculus. Default = "all".
dr.method	DR method to calculate. Possible values are "PCA", "tSNE", "DENSNE", "UMAP" and/or "DENSMAP". If PCA is calculated, rotation values are also stored in the 'fcs.SCE@metadata' (or separatelly if 'data' is a 'data.frame' instead a 'fcs.SCE' object).
num.threads	Number of threads for DR calculus. If NULL (default), all cores available minus one will be used. If this option is enable, reproducibility could be comprised.
perplexity.tsne	Value for perplexity parameter in tSNE calculation (more information). Default = 100.
n.neighbors.umap	Value for neighbors parameter in UMAP calculation (more information). Default = 50.

Examples

## Not run: 
fcs <- dim.reduction(fcs, dr.method = "tSNE", 
   markers.to.use = c("CD8", "CD27", "CCR4", "CD45RA", "CD4"))
fcs <- dim.reduction(fcs, dr.method = "UMAP", n.neighbors.umap = 10)
fcs <- dim.reduction(fcs, dr.method = c("pca", "Umap"))

## End(Not run)

jgarces02/FlowCT documentation built on March 28, 2023, 12:42 p.m.