Package index • BEAMR

All functions

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