scaden_process: Pre-processes training data

In PelzKo/immunedeconv2: Second generation methods for immune cell deconvolution

Pre-processes training data

Description

Training data needs to be processed before a model can be trained.

Usage

scaden_process(
  h5ad,
  temp_dir = NULL,
  bulk_gene_expression,
  var_cutoff = NULL,
  verbose = FALSE
)

Arguments

h5ad	File that should be processed. Must be in AnnData format (.h5ad)
temp_dir	The temporary directory to use for the computations (optional)
bulk_gene_expression	Bulk RNA-seq data. (genes x individuals)
var_cutoff	Filter out genes with a variance less than the specified cutoff. A low cutoff is recommended,this should only remove genes that are obviously uninformative.
verbose	Whether to produce an output on the console. (default: false)

Value

processed training file. (.h5ad format)

PelzKo/immunedeconv2 documentation built on Feb. 12, 2025, 4:16 p.m.