Man pages for brucemoran/somenone
R functions required by the somenone NextFlow nf-core pipeline
| anno_cgc_cna | Annotate CNA with cgc_gr IDs |
| anno_ens_cna | Annotate CNA with ENSembl IDs |
| at_least_two | Find consensus of at least two callers using GRanges... |
| bin_granges | Take input of a GRanges object, and use that seqinfo to bin... |
| bin_maker | Take input of a GRanges object, and use that seqinfo to bin... |
| cna_master_muts | Parse CN file and output as list |
| collapse_gr_list | Function to make master table mcols |
| download_chimerkb4 | Download and parse ChimerKB v4 for annotating known fusions |
| facets_cna_call | Standard Facets CNA call wrapper |
| facets_cna_consensus | Consensus CNA estimation and plotting with Facets input All... |
| facets_jointsegs_parse_to_gr | Parse jointsegs into GRanges object |
| findin_chimerkb4 | find ChimerKB data in user data |
| granges_sdin | Helper deals with setdiff, intersect to return full GRanges... |
| gridss_annotate_gr | Annotate a GRanges object from GRIDSS |
| gridss_bedpe_list | Produce a list of bedpe, from a list of breakpoint GRanges,... |
| gridss_parse_multi_vcf | Parse multi-sample VCF (recommended output of GRIDSS) |
| gridss_parse_plot | GRIDSS functions |
| gr_super_alt_plot | Wrapper of main functions |
| gr_super_set | Create GRanges 'superset' from GRanges per-sample, per-caller... |
| hello | Hello, World! |
| loh_summary | LOH summary: find LOH in GRanges |
| make_pairtree_input | Write output for pairtree based on mutations in master TSV... |
| make_pairtree_json | Write JSON for pairtree |
| master_intersect_cna_grlist | Find intersect from list of CNA GRanges |
| master_intersect_snv_grlist | Find intersect from list of SNV GRanges |
| master_mcols | Function to make master table mcols |
| mut_cn_to_pyclone | Parse mutation and CN input, creating a master table of... |
| output_out_list | Plotting and Output from 'out_list' object |
| parse_cn_list | Parse CN files and output as list |
| parse_input_df | find ChimerKB data in user data |
| plot_circos_sv | OmicCircos plotting from data.frame from GRIDSS bedpe |
| plot_consensus | Create plot of shared variants among samples |
| plot_from_tsv | Allow tunable reformatting of plots |
| plot_out_list | Plotting from 'out_list' object |
| plot_single | Create plot of shared variants among samples |
| prep_plot_circos_sv | OmicCircos plotting from data.frame from GRIDSS bedpe |
| process_in_list | Processing list of Facets input |
| rdata_gr_list | run function to make list of GRanges per caller |
| seqlengths_df | Create lengths of chromosomes for plotting |
| sub_hgvsp | Create single-letter HGVS protein annotation (VEP outputs... |
| summarise_master | Summarise master table |
| test_seqinfo | Test for seqinfo |
| variant_consensus | somatic_variant_consensus functions |
| vcf_parse_gr | Parses for VCFs into GRanges object |
| vcf_vep_ann_parse_soma_gr | Parses for VCFs annotated by VEP into GRanges object takes... |
