scaden (Single-cell assisted deconvolutional network) deconvolution of bulk data using an `screference`

Usage

scaden_deconvolute(
  bulk_data,
  scref,
  cache_path = "scaden_results",
  retrain = FALSE,
  ...
)

Arguments

bulk_data: a matrix of genes-by-samples with bulk mixtures
scref: an object of class `screference`
cache_path: path to cache the intermediate results
retrain: if TRUE, model is re-processed with the `bulk_data` reference and retrained
...: passed to scaden_scref if retrain = TRUE
a: tibble with deconvolution fractions

Note

Reference: Menden, Kevin, Mohamed Marouf, Sergio Oller et al., 2020. “Deep Learning–Based Cell Composition Analysis from Tissue Expression Profiles.” Science Advances 6 (30): eaba2619. https://doi.org/10.1126/sciadv.aba2619.

See also: https://github.com/theislab/AutoGeneS