Classify DLBCLs according to genetic subgroups of Chapuy et al. — classify_dlbcl

Use the feature weights from NMF model to assemble the binary matrix and classify DLBCL tumors based on C0-C5 system of Chapuy et al

Usage

classify_dlbcl_chapuy(
  these_samples_metadata,
  maf_data,
  seg_data,
  sv_data,
  projection = "grch37",
  output = "both"
)

these_samples_metadata: The metadata data frame that contains sample_id column with ids for the samples to be classified.
maf_data: The MAF data frame to be used for matrix assembling. At least must contain the first 45 columns of standard MAF format.
seg_data: The SEG data frame to be used for matrix assembling. Must be of standard SEG formatting, for example, as returned by get_cn_segments.
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.
projection: The projection of the samples. Only used to retrerive data through GAMBLR.data when it is not provided. Defaults to grch37.
output: The output to be returned after prediction is done. Can be one of predictions, matrix, or both. Defaults to both.

data frame, binary matrix, or both