Construct reduced 21-dimension feature vector for DLBCLass

This function is an R port of some of the pre-processing code in DLBCLass https://github.com/getzlab/DLBCL-Classifier

Usage

construct_reduced_winning_version(
  mutations_file = "inst/extdata/DLBCL.699.fullGSM.Sep_23_2022.tsv",
  fisher_test_result_file = "inst/extdata/fisher_exact_5x2.Sep_23_2022.combined.tsv",
  include_cn = TRUE,
  mutation_data,
  add_missing_features = FALSE
)

Arguments

add_missing_features

Set to TRUE to fill in missing features with zeroes

data

Data frame of mutation status from DLBCLass supplement

fisher_test_result

Fisher's test result from DLBCLass github repository

Value

a list of data frames with the full mutation features, collapsed 21-dimension meta-features and mutation-only (no CNV) features

Examples

if (FALSE) { # \dontrun{
original_dlbclass_features = construct_reduced_winning_version()
} # }