Collection of Curated Data for Genomic Analysis of Mature B-cell
Lymphomas in R
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘GAMBLR.data’ version 1.1.1
Help Pages
| annotate_hotspots | Annotate Hotspots. |
| 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. |
| check_excess_params | Check Excess Params |
| chromosome_arms_grch37 | Chromosome Arms grch37. |
| chromosome_arms_hg38 | Chromosome Arms hg38. |
| collate_results | Collate Results |
| colour_codes | Colour Codes |
| cool_overlaps | Cool overlap of data frames. |
| dhitsig_genes_with_weights | Double Hit Signature Genes With Weights. |
| ease | ID Ease |
| gambl_metadata | GAMBL Metadata |
| gene_blacklist | Genes Blacklist. |
| get_ashm_count_matrix | Get ASHM Count Matrix. |
| get_cn_segments | Get CN Segments. |
| get_coding_ssm | Get Coding SSMs |
| get_coding_ssm_status | Get Coding SSM Status. |
| get_colours | Get standardized colours for lymphoid cancers. |
| get_gambl_metadata | Get GAMBL Metadata. |
| get_genes | Get genes from one or more gene lists |
| get_manta_sv | Get Manta SVs |
| get_mapped_colours | Produce colour palettes from your metadata. |
| get_sample_cn_segments | Get Sample CN Segments. |
| 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 Samples. |
| get_ssm_by_samples | Get SSM By Samples. |
| grch37_all_gene_coordinates | Gene Coordinates for grch37 (all). |
| grch37_ashm_regions | GRCh37 ASHM Regions |
| 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_ashm_regions | hg38 ASHM Regions |
| 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. |
| hgnc2pfam.df | Mapping table between gene.symbol, uniprot.id, and pfam |
| hotspots_annotations | Hotspot Annotations |
| hotspot_regions_grch37 | grch37 Hotspot Regions. |
| hotspot_regions_hg38 | hg38 Hotspot Regions. |
| id | ID Ease |
| id_ease | ID Ease |
| id_ease, | ID Ease |
| lymphoma_genes | Lymphoma Genes v0.0 |
| lymphoma_genes_bl_v0.1 | Lymphoma Genes BL v0.1 |
| lymphoma_genes_bl_v_latest | Lymphoma Genes BL Latest |
| lymphoma_genes_comprehensive | Lymphoma Genes Comprehensive. |
| lymphoma_genes_dlbcl_v0.1 | Lymphoma Genes DLBCL v0.1 |
| lymphoma_genes_dlbcl_v_latest | Lymphoma Genes DLBCL Latest |
| lymphoma_genes_lymphoma_genes_v0.0 | Lymphoma Genes v0.0 |
| lymphoma_genes_mcl_v0.1 | Lymphoma Genes MCL v0.1 |
| lymphoma_genes_mcl_v_latest | Lymphoma Genes MCL Latest |
| mirage_metrics | Mirage Metrics |
| mutation.table.df | Default mapping table between mutation type (aka, variant classification) to mutation class |
| process_regions | Process Regions objects. |
| protein_domains | Protein Domains |
| reddy_genes | Reddy Genes. |
| region_to_chunks | Separate a chromosome region into chunks |
| review_hotspots | Review Hotspots. |
| sample_data | Sample Data |
| somatic_hypermutation_locations_GRCh37_v0.0 | Somatic Hypermutation Locations GRCh37 v0.0 |
| somatic_hypermutation_locations_GRCh37_v0.1 | Somatic Hypermutation Locations GRCh37 v0.1 |
| somatic_hypermutation_locations_GRCh37_v0.2 | Somatic Hypermutation Locations GRCh37 v0.2 |
| somatic_hypermutation_locations_GRCh37_v0.3 | Somatic Hypermutation Locations GRCh37 v0.3 |
| somatic_hypermutation_locations_GRCh37_v0.4 | Somatic Hypermutation Locations GRCh37 v0.4 |
| somatic_hypermutation_locations_GRCh37_v0.5 | Somatic Hypermutation Locations GRCh37 v0.5 |
| somatic_hypermutation_locations_GRCh37_v_latest | Somatic Hypermutation Locations GRCh37 Latest |
| somatic_hypermutation_locations_GRCh38_v0.0 | Somatic Hypermutation Locations GRCh38 v0.0 |
| somatic_hypermutation_locations_GRCh38_v0.1 | Somatic Hypermutation Locations GRCh38 v0.1 |
| somatic_hypermutation_locations_GRCh38_v0.2 | Somatic Hypermutation Locations GRCh38 v0.2 |
| somatic_hypermutation_locations_GRCh38_v0.3 | Somatic Hypermutation Locations GRCh38 v0.3 |
| somatic_hypermutation_locations_GRCh38_v0.4 | Somatic Hypermutation Locations GRCh38 v0.4 |
| somatic_hypermutation_locations_GRCh38_v0.5 | Somatic Hypermutation Locations GRCh38 v0.5 |
| somatic_hypermutation_locations_GRCh38_v_latest | Somatic Hypermutation Locations GRCh38 Latest |
| target_regions_grch37 | Target Regions grch37. |
| target_regions_hg38 | Target Regions hg38. |
| wright_genes_with_weights | Wright Genes With Weights. |