AutoGeneS deconvolution of bulk data using an `screference`

Usage

autogenes_deconvolute(
  bulk_data,
  scref,
  model = c("nusvr", "nnls", "linear")[1]
)

Arguments

bulk_data

a matrix of genes-by-samples with bulk mixtures

scref

an object of class `screference`

model

a model to run AutoGeneS. One of: `'nusvr'`, `'nnls'` or `'linear'`

Value

a tibble with deconvolution fractions

Note

Reference: Aliee, Hananeh, and Fabian J. Theis. 2021. “AutoGeneS: Automatic Gene Selection Using Multi-Objective Optimization for RNA-Seq Deconvolution.” Cell Systems 12 (7): 706-715.e4. https://doi.org/10.1016/j.cels.2021.05.006.

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