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Prepare data for CCI inference

prepare_data.Rd

filters data and then normalizes the gene expression

Usage

prepare_data(
  input_file,
  annot,
  sample_id = NULL,
  output_dir = ".",
  min_cells = 5,
  save_as_10x_format = TRUE
)

Arguments

input_file

path to seurat object (rds file)

annot

variable in metadata containing the cell annotation

sample_id

sample id to use for saving formatted CCI results (default = NULL; will determine sample id based on 'input_interactions' for this input_interactions has to be of the format 'cpdb__sample_id.csv')

output_dir

output directory for saving output (default = '.')

min_cells

Minimum number of cells required in each cell group for cell-cell communication (default = 5)

save_as_10x_format

Logical indicating whether the expression data needs to be saved in the 10x format (default=TRUE)