Function reference • GAMBLR

Annotations Functions used to annotate GAMBL data.
`annotate_driver_ssm()`	Annotate Driver SSM.
`annotate_hotspots()`	Annotate Hotspots.
`annotate_igh_breakpoints()`	Annotate IGH Breakpoints.
`annotate_recurrent_cnv()`	Annotate Recurrent CNVs.
`annotate_ssm_blacklist()`	Annotate SSM with Blacklists
`annotate_sv()`	Annotate SVs.
Bundled Data This is the bundled data used by GAMBLR.
`chromosome_arms_grch37`	Chromosome Arms grch37.
`chromosome_arms_hg38`	Chromosome Arms hg38.
`dhitsig_genes_with_weights`	Double Hit Signature Genes With Weights.
`gene_blacklist`	Genes Blacklist.
`grande_maf`	Grande et al. MAF.
`grch37_all_gene_coordinates`	Gene Coordinates for grch37 (all).
`grch37_gene_coordinates`	grch37 Gene Coordinates.
`grch37_lymphoma_genes_bed`	Lymphoma Genes (grch37).
`grch37_oncogene`	Oncogenes in grch37 genome build.
`grch37_partners`	grch37 Partner Genes.
`hg38_gene_coordinates`	hg38 Gene Coordinates.
`hg38_lymphoma_genes_bed`	Lymphoma Genes (hg38).
`hg38_oncogene`	Oncogenes in hg38 genome build.
`hg38_partners`	hg38 Partner Genes.
`hotspot_regions_grch37`	grch37 Hotspot Regions.
`hotspot_regions_hg38`	hg38 Hotspot Regions.
`lymphoma_genes_comprehensive`	Lymphoma Genes Comprehensive.
`reddy_genes`	Reddy Genes.
`target_regions_grch37`	Target Regions grch37.
`target_regions_hg38`	Target Regions hg38.
`wright_genes_with_weights`	Wright Genes With Weights.
cBioPortal Functions tailored to setting up a new study or updating an existing cBioPortal instance.
`cbioportal_create()`	Create cBioPortal Study.
`custom_caselist()`	Custom cBioPortal case list.
`finalize_study()`	Finalize Study (cBioPortal).
`get_study_info()`	Get Study Info.
`setup_expreession_data()`	Setup Expression Data (cBioPortal).
`setup_fusions()`	Setup Fusions (cBioPortal).
`setup_study()`	Setup Study (cBioPortal).
`study_check()`	Study Check (cBioPortal).
Checks GAMBLR functions that fall under the check category.
`check_gambl_metadata()`	Check GAMBL Metadata.
`check_gamblr_config()`	Check GAMBLR Config.
`check_host()`	Check Host.
`check_remote_configuration()`	Check Remote Configuration.
`fread_maf()`	Fread MAF.
Get Data A collection of functions used to retrieve data of different types.
`get_ashm_count_matrix()`	Get ASHM Count Matrix.
`get_bams()`	Get BAMs.
`get_cn_segments()`	Get CN Segments.
`get_cn_states()`	Get CN States.
`get_coding_ssm()`	Get Coding SSM.
`get_coding_ssm_status()`	Get Coding SSM Status.
`get_combined_sv()`	Get Combined SV.
`get_excluded_samples()`	Get Excluded Samples.
`get_gambl_colours()`	Get GAMBL Colours.
`get_gambl_metadata()`	Get GAMBL metadata.
`get_gene_cn_and_expression()`	Get Gene CN and Expression.
`get_gene_expression()`	Get Gene Expression.
`get_lymphgen()`	Get Lymphgen.
`get_manta_sv()`	Get Manta SVs
`get_manta_sv_by_sample()`	Get Manta SV By Sample.
`get_manta_sv_by_samples()`	Get Manta SV By Samples.
`get_mutation_frequency_bin_matrix()`	Mutation Frequency Heatmap
`get_sample_cn_segments()`	Get Sample CN Segments.
`get_sample_wildcards()`	Get Sample Wildcards
`get_samples_md5_hash()`	Generate md5 Hash For Samples
`get_ssh_session()`	Get SSH Session.
`get_ssm_by_patients()`	Get SSM By Patients.
`get_ssm_by_sample()`	Get SSM By Sample.
`get_ssm_by_samples()`	Get SSM By Samples.
`get_ssm_by_region()`	Get SSM By Region.
`get_ssm_by_regions()`	Get SSM By Regions.
Plotting Functions used for visualizing GAMBL data.
`ashm_multi_rainbow_plot()`	ASHM Multi-panel Rainbow Plot
`ashm_rainbow_plot()`	ASHM Rainbow Plot
`calc_mutation_frequency_sliding_windows()`	Calculate Mutation Frequency By Sliding Window.
`cnvKompare()`	Compare segmented data for multiple samples.
`comp_report()`	sample-level SV/SSM/CN reports in PDF
`copy_number_vaf_plot()`	CN VAF Plot
`fancy_alignment_plot()`	Plot Alignment Metrics
`fancy_circos_plot()`	SSM and SV Circos Plot.
`fancy_cnbar()`	Copy Number states barplot
`fancy_ideogram()`	genome-wide ideogram annotated with SSM and CN information
`fancy_multisamp_ideogram()`	Genome-wide ideogram (CN segments) for multiple samples.
`fancy_propcov_plot()`	Proportional Coverage Plot.
`fancy_proportions_plot()`	Proportional Metrics Plot.
`fancy_qc_plot()`	Plot Quality Control Metrics.
`fancy_snv_chrdistplot()`	n SNVs per chromosome plot
`fancy_sv_sizedens()`	Structural Variants Size Plot.
`fancy_v_chrcount()`	n variants per chromosome plot.
`fancy_v_count()`	Total n variants count plot.
`fancy_v_sizedis()`	Variant size distribution plot
`focal_cn_plot()`	Copy Number Segments Plot
`FtestCNV()`	Fishers Exact Test (CNV).
`plot_sample_circos()`	Sample-level Circos Plot
`prettyChromoplot()`	Chromosome Plot
`prettyCoOncoplot()`	Side-by-side Oncoplots
`prettyForestPlot()`	Forest Plot.
`prettyGeneCloud()`	Gene Cloud Plot
`prettyOncoplot()`	Oncooplot
`prettyRainfallPlot()`	Rainfall Plot
`pretty_lollipop_plot()`	Lollipop Plot
`splendidHeatmap()`	Heatmap
`theme_Morons()`	Morons Theme
Statistical testing and Computing Functions used for executing statistical and other calculations on incoming GAMBL data.
`FtestCNV()`	Fishers Exact Test (CNV).
`calc_mutation_frequency_sliding_windows()`	Calculate Mutation Frequency By Sliding Window.
`calculate_pga()`	Calculate proportion of genome altered by CNV.
`cnvKompare()`	Compare segmented data for multiple samples.
`count_ssm_by_region()`	Count SSM In A Region
`estimate_purity()`	Estimate Purity.
`prettyForestPlot()`	Forest Plot.
Utilities A collection of functions that fall under the utility category.
`adjust_ploidy()`	Adjust ploidy for samples with CNV data.
`assemble_file_details()`	Assemble File Details.
`assign_cn_to_ssm()`	Assign CN to SSM.
`cleanup_maf()`	Cleanup MAF.
`consolidate_lymphgen()`	Consolidate Lymphgen.
`collate_lymphgen()`	Collate Lymphgen.
`collate_results()`	Collate Results
`fetch_output_files()`	Fetch Output Files.
`find_expected_outputs()`	Find Expected Outputs.
`find_files_extract_wildcards()`	Find Files Extract Wildcards
`gene_to_region()`	Gene To Region.
`genome_to_exome()`	Genome To Exome.
`intersect_maf()`	Intersect MAF.
`liftover_bedpe()`	Liftover Bedpe.
`maf_to_custom_track()`	Maf To Custom Track.
`make_igv_snapshot()`	Make IGV Snapshot
`populate_each_tool_result()`	Populate Each Tool Results.
`populate_tool_results()`	Populate Tool Results.
`region_to_bins()`	Region To Bins.
`region_to_gene()`	Region To Gene.
`review_hotspots()`	Review Hotspots.
`sanitize_maf_data()`	Convert mutation data to a shareable format.
`sv_to_bedpe_file()`	SV To BED File.
`sv_to_custom_track()`	SV To Custom Track.
`supplement_maf()`	Supplement MAF.
`tidy_gene_expression()`	Tidy gene Expression.
`tidy_lymphgen()`	Tidy Lymphgen.
`view_mutation_igv()`	View a variant in IGV
`write_sample_set_hash()`	Write Sample Set Hash

Reference

Annotations

Bundled Data

cBioPortal

Checks

Get Data

Plotting

Statistical testing and Computing

Utilities