Access results of the Genomic Analysis of Mature B-cell
Lymphomas
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Documentation for package ‘GAMBLR.results’ version 1.1.1
Help Pages
| add_icgc_metadata | Add ICGC metadata. |
| annotate_hotspots | Annotate Hotspots. |
| annotate_maf_triplet | Annotate MAF with triplet context |
| annotate_ssm_blacklist | Annotate SSM with Blacklists |
| annotate_ssm_motif_context | Annotate mutations target motif |
| ashm_multi_rainbow_plot | ASHM Multi-panel Rainbow Plot |
| ashm_rainbow_plot | ASHM Rainbow Plot |
| assemble_file_details | Assemble File Details. |
| assign_cn_to_ssm | Assign CN to SSM. |
| calc_mutation_frequency_bin_region | Calculate Mutation Frequency By Sliding Window. |
| calc_mutation_frequency_bin_regions | Mutation counts across sliding windows for multiple regions. |
| cbio_create | Create cBioPortal Study. |
| cbio_custom_caselist | Custom cBioPortal case list. |
| cbio_finalize_study | Finalize Study (cBioPortal). |
| cbio_setup_expreession_data | Setup Expression Data (cBioPortal). |
| cbio_setup_fusions | Setup Fusions (cBioPortal). |
| cbio_setup_study | Setup Study (cBioPortal). |
| cbio_study_check | Study Check (cBioPortal). |
| check_gamblr_config | Check GAMBLR Config. |
| check_gambl_metadata | Check GAMBL Metadata. |
| check_gene_expression | Check Gene Expression. |
| check_host | Check Host. |
| check_remote_configuration | Check Remote Configuration. |
| cleanup_maf | Cleanup MAF. |
| collate_lymphgen | Collate Lymphgen. |
| collate_results | Collate Results |
| consolidate_lymphgen | Consolidate Lymphgen. |
| ease | ID Ease |
| estimate_purity | Estimate Purity. |
| fetch_output_files | Fetch Output Files. |
| find_expected_outputs | Find Expected Outputs. |
| find_files_extract_wildcards | Find Files Extract Wildcards |
| get_all_coding_ssm | Get all Coding SSMs |
| get_ashm_count_matrix | Get ASHM Count Matrix. |
| get_bams | Get BAMs. |
| get_cnv_and_ssm_status | Get CNV and coding SSM combined status |
| 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_metadata | Get GAMBL metadata. |
| get_gambl_outcomes | Get GAMBL Outcomes. |
| 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_raw_expression_counts | Get Raw Expression Counts |
| get_samples_md5_hash | Generate md5 Hash For Samples |
| get_sample_cn_segments | Get Sample CN Segments. |
| get_sample_wildcards | Get Sample Wildcards |
| get_ssh_session | Get SSH Session. |
| get_ssm_by_patients | Get SSM By Patients. |
| get_ssm_by_region | Get SSM By Region. |
| get_ssm_by_regions | Get SSM By Regions. |
| get_ssm_by_sample | Get SSM By Sample. |
| get_ssm_by_samples | Get SSM By Samples. |
| get_study_info | Get Study Info. |
| id | ID Ease |
| id_ease | ID Ease |
| id_ease, | ID Ease |
| link_seq_types | Link seq type IDs |
| og_get_gambl_metadata | Get GAMBL metadata. |
| populate_each_tool_result | Populate Each Tool Results. |
| populate_tool_results | Populate Tool Results. |
| pretty_lymphoplot | LymphGen feature visualization. |
| tidy_gene_expression | Tidy gene Expression. |
| write_sample_set_hash | Write Sample Set Hash |