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 |