Run GO enrichment preprocessing for MANGO — MANGO

Reads DEG lists, runs clusterProfiler::enrichGO (BP), writes per-case GO tables, then calls the preprocessing shell script and writes the resulting preprocessing list.

Usage

MANGO_PREPROCESSING(
  DEG_list_path,
  GO_list_path,
  MANGO_PREPROCESSING_list_path,
  ref_genome,
  core,
  filepath
)

Arguments

DEG_list_path: Path to a table listing DEG files (one file per row).
GO_list_path: Output path to write the list of generated GO result files.
MANGO_PREPROCESSING_list_path: Output path to write the list of generated MANGO preprocessing result files.
ref_genome: Reference genome code. Use "mm" for mouse or "hs" for human.
core: Number of cores to pass to the preprocessing shell script.
filepath: Base directory where CODE/init_MANGO_PREPROCESSING.sh exists.

Value

Writes output files to disk. Returns NULL invisibly.

Examples

stopifnot(is.function(MANGO_PREPROCESSING))
if (FALSE) { # \dontrun{
MANGO_PREPROCESSING(
  DEG_list_path = "input_DEG_list.txt",
  GO_list_path = "input_DEG_GO_list.txt",
  MANGO_PREPROCESSING_list_path = "MANGO_PREPROCESSING_list.txt",
  ref_genome = "mm",
  core = 1,
  filepath = "."
)
} # }