Format the input counts before creating the CONGAS+ object

This function takes in input a SummarizedExperiment object with rowranges and and creates a tibble with counts needed to create the Rcongas object.

create_congas_tibble(
  counts,
  features = NULL,
  modality = "ATAC",
  save_dir = NULL,
  output_file = "counts_final.tsv"
)

Arguments

counts

(Required). Count matrix with cells in columns and genes/bins in rows.

features

(Required) Dataframe containing columns chr, from, to and (only if RNA) gene.

modality.

Default 'ATAC' It has to be either ATAC or RNA based on the content of the count matrix.

output_dir.

Optional. Default = NULL. Directory where to save the tibble as a tsv file. If NULL, the tibble object is only returned.

output_file.

Optional, default is 'counts_final.tsv'. Name to give to the counts file. Note that this has not effect is output_dir is NULL.