Construct LymphGenerator matrix — classify_dlbcl_lymphgenerator • GAMBLR.predict

Use the LymphGenerator features to construct matrix. Optionally, flatten some features having the same biological information.

Usage

classify_dlbcl_lymphgenerator(
  these_samples_metadata,
  maf_data,
  sv_data,
  seg_data,
  seq_type = "genome",
  projection = "grch37",
  output = "matrix",
  drop_after_flattening = FALSE
)

Arguments

these_samples_metadata: The metadata data frame that contains sample_id column with ids for the samples to be classified. Must also contain column pathology.
maf_data: The MAF data frame to be used for matrix assembling. At least must contain the first 45 columns of standard MAF format.
sv_data: The SV data frame to be used for matrix assembling. Must be of standard BEDPE formatting, for example, as returned by get_combined_sv.
seg_data: The SEG data frame to be used for matrix assembling. Must be of standard SEG formatting, for example, as returned by get_sample_cn_segments. Must be already adjusted for ploidy.
seq_type: String of the seq type for the sample set.
projection: String of projection of the samples. Only used to retrieve data through GAMBLR.data when it is not provided. Defaults to grch37.
output: The output to be returned. Currently only matrix is supported.
drop_after_flattening: Boolean on whether to remove features (rows) after flattening. Defaults to FALSE.

Value

binary matrix