Build Model Cell2location

Build Model Cell2location

Usage

build_model_cell2location(
  single_cell_obj,
  epochs = 250,
  assay_sc = "counts",
  batch_id_col = "sample_id",
  cell_type_col = "celltype_major",
  cell_count_cutoff = 5,
  cell_percentage_cutoff = 0.03,
  nonz_mean_cutoff = 1.12,
  gpu = TRUE
)

Arguments

single_cell_obj

SingleCellExperiment containing reference expression

epochs

number of epochs to train the network

assay_sc

assay to extract

batch_id_col

batch_id_col column

cell_type_col

column of single_cell_obj containing cell type labels

cell_count_cutoff

cell2location parameter

cell_percentage_cutoff

cell2location parameter

nonz_mean_cutoff

cell2location parameter

gpu

whether to train on GPU