Get Lymphgen. — get_lymphgen • GAMBLR

Get a specific flavour of LymphGen from the main GAMBL outputs.

get_lymphgen(
  these_samples_metadata,
  flavour,
  return_feature_matrix = FALSE,
  return_feature_annotation = FALSE,
  lymphgen_file,
  keep_all_rows = FALSE,
  keep_original_columns = FALSE
)

Arguments

these_samples_metadata: A metadata table to auto-subset the data to samples in that table before returning.
flavour: Lymphgen flavour.
return_feature_matrix: Boolean parameter, default is FALSE.
return_feature_annotation: Boolean parameter, default is FALSE.
lymphgen_file: Path to lymphgen file.
keep_all_rows: Boolean parameter, default is FALSE.
keep_original_columns: Boolean parameter, default is FALSE.

Value

A data frame.

Details

Get a specific flavour of LymphGen from the main GAMBL outputs and tidy the composites. Optionally return a matrix of features instead

Examples

if (FALSE) {
lymphgens = get_lymphgen(flavour = "no_cnvs.no_sv.with_A53")
}