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Process profiles for each column in the CTSS dataset and save results

plc_profile.Rd

This function processes the profiles for each column in a RangedSummarizedExperiment object (`ctss_rse`), computes the count profiles, and calls a chromosome-specific function to handle individual chromosomes and save the results.

Usage

plc_profile(
  ctss_rse,
  regions_gr,
  output_dir,
  profile_dir_name,
  file_type = "npz",
  python_path = NULL,
  addtn_to_filename = "",
  save_count_profiles = FALSE,
  num_cores = NULL,
  processing_method = "multisession",
  ext_dis
)

Arguments

ctss_rse

A RangedSummarizedExperiment object containing CTSS counts.

regions_gr

A GRanges or GRangesList object containing genomic regions.

output_dir

The directory where output files will be saved.

profile_dir_name

The directory name for the output.

file_type

The output file format. One of: "parquet" (default), "csv", or "npz".

python_path

The path to the Python executable. If NULL, the default Python environment will be used.

addtn_to_filename

A string to add to the output filename.

save_count_profiles

Logical flag indicating whether count profiles should be saved.

num_cores

The number of cores to use for parallel processing. (default: "plc_log_profile").

ext_dis

Integer value for extending the distance used in profile computations.