beam_dat                Pediatric T-ALL Clinical Data from COG trial
                        AALL0434
beam_dat_sm             Pediatric T-ALL Clinical Data from COG trial
                        AALL0434
beam_specs              Pediatric T-ALL BEAM Analysis Specs Data from
                        COG trial AALL0434
beam_specs_sm           Pediatric T-ALL BEAM Analysis Specs Data from
                        COG trial AALL0434
beam_stats              Pediatric T-ALL Clinical Data from COG trial
                        AALL0434
beam_stats_sm           Pediatric T-ALL Clinical Data from COG trial
                        AALL0434
check_beam_specs        Check that beam.specs satisfies all necessary
                        conditions
check_list_class        Check that each element of a list is of a
                        required class
clean_Bmtx              Clean up bootstrap coefficient matrix
clinf                   Pediatric T-ALL Clinical Data from COG trial
                        AALL0434
compute_beam_stats      Compute bootstrap model coefficients for BEAM
compute_feature_pvalues
                        Compute feature level p-values from BEAM
                        statistics
compute_set_pvalues     Compute BEAMR p-values for sets
extend_set_data         Extend set definition data with genes on the
                        same row separated by commas, semicolons,
                        slashes, etc
extract_beam_stats      Extract beam stats for a specific set
find_id_clm             Find the column of mtch.data with the most rows
                        containing an element of ids
gen_beam_plot_list      Generate BEAM Plot List
get_id_index            For each row of the data.frame main.data, find
                        the index of the matching element in vector ids
omicann                 Pediatric T-ALL Omics Annotation Data from COG
                        trial AALL0434
omicdat                 Pediatric T-ALL Omics Data from COG trial
                        AALL0434
plot_beam_boot          Plot bootstrap output for BEAM sets
plot_beam_clin          Plot BEAM Sets
plot_feat_clin          Plot BEAM Feature
prep_beam_data          Prepare data for BEAM analysis
prep_beam_plot          Prepare for BEAM plotting
prep_beam_specs         Prepare beam.specs
print.beam.data         Print summary information about a beam.data
                        object
print.beam.stats        Print summary information about beam.stats
                        object
setdat                  Map of Pediatric Data from COG trial AALL0434
specs                   Pediatric T-ALL BEAMR Analysis Specs Data from
                        COG trial AALL0434
subset_beam_result      Subset beam.stats Result
