Man pages for Wedge-lab/dpclust3p
Dirichlet Process Clustering Pre-Processing Package
| alleleCount | Run alleleCount |
| ascatNgsToBattenberg | Transform ASCAT NGS output into Battenberg |
| ascatToBattenberg | Transform ASCAT output into Battenberg |
| calc_power | Calculate power to call subclones. |
| collate_bb_subclones | This function takes a Battenberg styled data.frame, pulls out... |
| concat_files | Concatenate split files |
| createPng | Create a PNG file |
| createProjectFile | Creates a DPClust project master file |
| dpclust3p | Dirichlet Process Clustering PreProcessing Package |
| dpIn2vcf | DPClust input file to vcf |
| dumpCounts.Broad | Dump allele counts from vcf - Broad ICGC pancancer pipeline |
| dumpCounts.cgpPindel | Dump allele counts from vcf - CGP Pindel indel pipeline |
| dumpCounts.DKFZ | Dump allele counts from vcf - DKFZ ICGC pancancer pipeline |
| dumpCounts.ICGCconsensusIndel | Dump allele counts from vcf - ICGC pancancer consensus indel... |
| dumpCounts.ICGCconsensusSNV | Dump allele counts from vcf - ICGC pancancer consensus SNV... |
| dumpCounts.Muse | Dump allele counts from vcf - MuSE ICGC pancancer pipeline |
| dumpCounts.mutect | Dump allele counts from vcf - Mutect |
| dumpCounts.Sanger | Dump allele counts from vcf - Sanger ICGC pancancer pipeline |
| dumpCounts.scalpel | Dump allele counts from vcf - Scalpel |
| dumpCounts.StrelkaIndel | Dump allele counts from vcf - Strelka indel pipeline |
| extend_bb_cn_categories | This function extends existing categories by a list of sizes |
| filterForDeaminase | Convenience function that filters a with tri-nucleotide... |
| filterForSignature | Filter a with tri-nucleotide context annotated list of loci... |
| getAltAllele | Obtain alt allele for all variants as a vector |
| get_bb_cn_catalog | Count how often each of the categories is present in this... |
| getTrinucleotideContext | Obtain tri-nucleotide context. It reads in the supplied loci... |
| identifyKataegis | Identify Kataegis events in SNV mutation data |
| mutationBurdenToMutationCopyNumber | Mutation burden to mutation copy number |
| mutationCopyNumberToMutationBurden | Mutation copy number to mutation burden |
| mut_cn_phasing | Phase mutation to SNP/copy number |
| mut_mut_phasing | Phase mutation to mutation |
| parseFai | Parse genome index |
| parseIgnore | Parse chromosomes to ignore file |
| plot_ccf_hist | Plot cancer cell fraction histogram |
| plot_mcn_hist | Plot mutation copy number histogram |
| plot_vaf_hist | Plot allele frequency histogram |
| runGetDirichletProcessInfo | Create the DPClust input file |
| split_by_chrom | Split a file per chromosome |
| vcf2loci | Transform vcf to loci file |
