Bootstrap Evaluation of Association Matrices

[Up] [Top]

Documentation for package ‘BEAMR’ version 1.1.0

Help Pages

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