Run the MANGO analysis pipeline — MANGO

Orchestrates preprocessing (optional), term listing, comparison, and separation. Supports both single- and multi-condition workflows.

Usage

MANGO_ANALYSIS(
  filepath,
  DEG_list_name,
  ref_genome,
  core = 1,
  PASSED_RATIO,
  PASSED_NUM,
  similarity,
  FC = 2,
  condition = 1,
  dynamic_analyisis = "F",
  preprocessing = "F"
)

Arguments

filepath: Working directory path.
DEG_list_name: DEG list filename under filepath.
ref_genome: Reference genome code ("mm" or "hs").
core: Number of cores.
PASSED_RATIO: Passed dependency ratio threshold.
PASSED_NUM: Passed dependency count threshold.
similarity: Similarity cutoff (%).
FC: Fold-change ratio cutoff.
condition: condition index for dynamic analysis.
dynamic_analyisis: "T" or "F" to enable multi-range filtering.
preprocessing: "T" or "F" to run preprocessing inside this function.

Value

Writes output files to disk. Returns NULL invisibly.

Examples

stopifnot(is.function(MANGO_ANALYSIS))
if (FALSE) { # \dontrun{
MANGO_ANALYSIS(
  filepath=".",
  DEG_list_name="input_DEG_list.txt",
  ref_genome="mm",
  core=1,
  PASSED_RATIO=15,
  PASSED_NUM=4,
  similarity=70
)
} # }