Collection of functions that consist of the core functionality
of GAMBLR
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Documentation for package ‘GAMBLR.utils’ version 1.1.1
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| adjust_ploidy | Adjust ploidy for samples with CNV data. |
| annotate_driver_ssm | Annotate Driver SSM. |
| annotate_igh_breakpoints | Annotate IGH Breakpoints. |
| annotate_intrachromosomal_sv | Annotate intrachromosomal SV. |
| annotate_recurrent_cnv | Annotate Recurrent CNVs. |
| annotate_sv | Annotate SVs. |
| build_browser_hub | Build UCSC browser track hub |
| 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 |
| fread_maf | Fread MAF. |
| FtestCNV | Fishers Exact Test (CNV). |
| gene_to_region | Gene To Region. |
| genome_to_exome | Genome To Exome. |
| intersect_maf | Intersect MAF. |
| liftover | Liftover. |
| maf_to_custom_track | Maf To Custom Track. |
| make_igv_snapshot | Make IGV Snapshot |
| region_to_bins | Region To Bins. |
| region_to_gene | Region To Gene. |
| sanitize_maf_data | Convert mutation data to a shareable format. |
| ssm_to_proteinpaint | MAF to ProteinPaint table |
| supplement_maf | Supplement MAF. |
| sv_to_bedpe_file | SV To BED File. |
| sv_to_custom_track | SV To Custom Track. |
| tidy_lymphgen | Tidy Lymphgen. |
| view_mutation_igv | View a variant in IGV |