Package: BEAMR 1.1.0.9000

BEAMR: Bootstrap Evaluation of Association Matrices

A bootstrap-based approach to integrate multiple forms of high dimensional genomic data with multiple clinical endpoints. This method is used to find clinically meaningful groups of genomic features, such as genes or pathways. A manuscript describing this method is in preparation.

Authors:Anna Eames Seffernick [aut, cre, cph], Stanley Pounds [aut], Xueyuan Cao [aut]

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BEAMR.pdf |BEAMR.html✨
BEAMR/json (API)
NEWS

# Install 'BEAMR' in R:
install.packages('BEAMR', repos = c('https://annaseffernick.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/annaseffernick/beamr/issues

Datasets:
  • 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
  • clinf - Pediatric T-ALL Clinical Data from COG trial AALL0434
  • omicann - Pediatric T-ALL Omics Annotation Data from COG trial AALL0434
  • omicdat - Pediatric T-ALL Omics Data from COG trial AALL0434
  • setdat - Map of Pediatric Data from COG trial AALL0434
  • specs - Pediatric T-ALL BEAMR Analysis Specs Data from COG trial AALL0434

On CRAN:

18 exports 5 stars 1.40 score 148 dependencies 1 scripts 286 downloads

Last updated 2 months agofrom:20f26a4f84. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 29 2024
R-4.5-winOKAug 29 2024
R-4.5-linuxOKAug 29 2024
R-4.4-winOKAug 29 2024
R-4.4-macOKAug 29 2024
R-4.3-winOKAug 29 2024
R-4.3-macOKAug 29 2024

Exports:check_beam_specscheck_list_classclean_Bmtxcompute_beam_statscompute_feature_pvaluescompute_set_pvaluesextend_set_dataextract_beam_statsfind_id_clmgen_beam_plot_listget_id_indexplot_beam_bootplot_beam_clinplot_feat_clinprep_beam_dataprep_beam_plotprep_beam_specssubset_beam_result

Dependencies:abindaskpassbackportsbase64encbitbit64bootbroombslibcachemcarcarDataclicliprcodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkcurldata.tableDerivdigestdoBydplyrevaluateexactRankTestsfansifarverfastmapfontawesomeforcatsforeachformula.toolsfsgenericsggmosaicggplot2ggpubrggrepelggsciggsignifggtextglmnetgluegridExtragridtextgtablehavenhighrhmshtmltoolshtmlwidgetshttrisobanditeratorsjomojpegjquerylibjsonlitekm.ciKMsurvknitrlabelinglaterlatticelazyevallifecyclelme4logistfmagrittrmarkdownMASSMatrixMatrixModelsmaxstatmemoisemgcvmicemicrobenchmarkmimeminqamitmlmodelrmunsellmvtnormnlmenloptrnnetnumDerivopenssloperator.toolsordinalpanpbkrtestpillarpkgconfigplotlyplyrpngpolynomprettyunitsproductplotsprogresspromisespurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreadrrlangrlistrmarkdownrpartrstatixsassscalesshapeSparseMstringistringrsurvivalsurvminersurvMiscsystibbletidyrtidyselecttinytextzdbucminfutf8vctrsviridisLitevroomwithrxfunXMLxml2xtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Pediatric T-ALL Clinical Data from COG trial AALL0434beam_dat
Pediatric T-ALL Clinical Data from COG trial AALL0434beam_dat_sm
Pediatric T-ALL BEAM Analysis Specs Data from COG trial AALL0434beam_specs
Pediatric T-ALL BEAM Analysis Specs Data from COG trial AALL0434beam_specs_sm
Pediatric T-ALL Clinical Data from COG trial AALL0434beam_stats
Pediatric T-ALL Clinical Data from COG trial AALL0434beam_stats_sm
Check that beam.specs satisfies all necessary conditionscheck_beam_specs
Check that each element of a list is of a required classcheck_list_class
Clean up bootstrap coefficient matrixclean_Bmtx
Pediatric T-ALL Clinical Data from COG trial AALL0434clinf
Compute bootstrap model coefficients for BEAMcompute_beam_stats
Compute feature level p-values from BEAM statisticscompute_feature_pvalues
Compute BEAMR p-values for setscompute_set_pvalues
Extend set definition data with genes on the same row separated by commas, semicolons, slashes, etcextend_set_data
Extract beam stats for a specific setextract_beam_stats
Find the column of mtch.data with the most rows containing an element of idsfind_id_clm
Generate BEAM Plot Listgen_beam_plot_list
For each row of the data.frame main.data, find the index of the matching element in vector idsget_id_index
Pediatric T-ALL Omics Annotation Data from COG trial AALL0434omicann
Pediatric T-ALL Omics Data from COG trial AALL0434omicdat
Plot bootstrap output for BEAM setsplot_beam_boot
Plot BEAM Setsplot_beam_clin
Plot BEAM Featureplot_feat_clin
Prepare data for BEAM analysisprep_beam_data
Prepare for BEAM plottingprep_beam_plot
Prepare beam.specsprep_beam_specs
Print summary information about a beam.data objectprint.beam.data
Print summary information about beam.stats objectprint.beam.stats
Map of Pediatric Data from COG trial AALL0434setdat
Pediatric T-ALL BEAMR Analysis Specs Data from COG trial AALL0434specs
Subset beam.stats Resultsubset_beam_result