Provide helper functions for GAMBLR-based packages
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Documentation for package ‘GAMBLR.helpers’ version 1.1.1
Help Pages
| bins_to_bedgraph | Bins to bed graph. |
| cache_output | Cache output. |
| calculate_tmb | Calculate tumour mutation burden. |
| check_config_value | Check Config Value. |
| check_file_details | Check file details |
| cnames | Required columns in bedpe. |
| coding_class | Coding+Silent variants classification. |
| coding_vc | Coding variants classification. |
| colour_aliases | Color code aliases. |
| compare_coding_mutation_pattern | Compare pattern of coding mutations. |
| copy_no_clobber | Copy not clobber. |
| create_onco_matrix | Create onco matrix from maf data. |
| fuzzy_match_mafs | Fuzzy match mafs |
| gene_mutation_tally | Tally coding mutations load. |
| get_gambl_colours | Get GAMBL Colours. |
| get_template_wildcards | Get template wildcards. |
| get_unmatched_normals | Get unmatched normals. |
| grob_wildcards | Glob wildcards. |
| handle_metadata | Handle metadata from bundled packages. |
| maf_header | Column names in maf. |
| normalize_expression_data | Normalize Expression Data |
| rainfall_conv | Reverse mappings. |
| required_cols | Required columns in metadata. |
| sanity_check_metadata | Sanity Check Metadata. |
| socketWrite | Socket write. |
| standardize_chr_prefix | Standardize Chromosome Prefix. |
| subset_cnstates | Subset CN States. |
| theme_Morons | Morons Theme |
| trim_scale_expression | Trim Scale Expressions. |
| vc_nonSynonymous | Non-synonymous variants classification. |
| web_initialize_gambl_site | Web Initialize GAMBL Site. |