API for Wedge-lab/battenberg
Battenberg subclonal copy number caller
| Global functions | |
|---|---|
| .onLoad | Source code |
| GetChromosomeBAFs | Man page Source code |
| GetChromosomeBAFs_SNP6 | Man page Source code |
| GetNearestCorners_bestOption | Source code |
| PottsCompact | Source code |
| adjustSegmValues | Source code |
| allele_ratio_plot | Man page |
| assert.file.exists | Source code |
| battenberg | Man page Source code |
| calc_BAF_Pvalue | Source code |
| calc_LogR_Pvalue | Source code |
| calc_Pvalue_binomial_twotailed | Source code |
| calc_Pvalue_t_twotailed | Source code |
| calc_binomial_prob | Source code |
| calc_distance | Source code |
| calc_distance_clonal | Source code |
| calc_ln_likelihood_ratio | Source code |
| calc_ploidy | Source code |
| calc_psi_t | Source code |
| calc_rho_psi_refit | Man page Source code |
| calc_square_distance | Source code |
| calc_standardised_error | Source code |
| calc_total_cn_major | Source code |
| calc_total_cn_minor | Source code |
| calculate_bb_total_cn | Source code |
| callChrXsubclones | Man page Source code |
| callSubclones | Man page Source code |
| call_multisample_MSAI | Man page Source code |
| cel2baf.logr | Man page Source code |
| cell_line_baf_logR | Source code |
| cell_line_reconstruct_normal | Source code |
| check.imputeinfofile | Man page Source code |
| clonal_findcentroid.plot | Source code |
| cnfit_to_refit_suggestions | Man page Source code |
| collapse_bafsegmented_to_segments | Source code |
| combine.baf.files | Man page Source code |
| combine.impute.output | Man page Source code |
| compact | Source code Source code |
| concatenateAlleleCountFiles | Source code |
| concatenateBAFfiles | Source code |
| concatenateG1000SnpFiles | Source code |
| concatenateImputeFiles | Source code |
| convert.impute.input.to.beagle.input | Man page Source code |
| coverage_plot | Man page |
| create.baf.plot | Source code |
| create.bb.plot.average | Source code |
| create.bb.plot.subclones | Source code |
| create.haplotype.plot | Source code |
| create.segmented.plot | Source code |
| create.subclonal.cn.plot | Source code |
| create_distance_matrix | Source code |
| create_distance_matrix_clonal | Source code |
| determine_copynumber | Source code |
| estimate_psi | Source code |
| estimate_rho | Source code |
| exactPcf | Source code |
| filterMarkS4 | Source code |
| findEst | Source code |
| findMarks | Source code |
| find_centroid_of_global_minima | Source code |
| fit.copy.number | Man page Source code |
| gc.correct | Man page Source code |
| gc.correct.wgs | Man page Source code |
| gc.correct.wgs.germline | Source code |
| generate.impute.input.snp6 | Man page Source code |
| generate.impute.input.wgs | Man page Source code |
| generate.impute.input.wgs.germline | Source code |
| germline_baf_logR | Source code |
| germline_reconstruct_normal | Source code |
| get.chrom.names | Man page Source code |
| get.psi.rho.from.ref.seg | Source code |
| getAlleleCounts | Man page Source code |
| getBAFsAndLogRs | Man page Source code |
| getMad | Source code |
| get_multisample_phasing | Man page Source code |
| get_new_bounds | Source code |
| get_segment_info | Source code |
| infer_gender_birdseed | Man page Source code |
| input_known_haplotypes | Man page Source code |
| is.segment.clonal | Source code |
| load.rho.psi.file | Source code |
| logr2tumcn | Source code |
| make_posthoc_plots | Man page Source code |
| markWithPotts | Source code |
| mask_high_cn_segments | Man page Source code |
| medianFilter | Source code |
| merge_segments | Source code |
| orderEdges | Source code |
| parse.imputeinfofile | Man page Source code |
| parseSNP6refFile | Source code |
| plot.gw.subclonal.cn | Source code |
| plot.haplotype.data | Man page Source code |
| prepare_snp6 | Man page Source code |
| prepare_wgs | Man page Source code |
| prepare_wgs_cell_line | Source code |
| prepare_wgs_germline | Source code |
| psi2psit | Source code |
| psit2psi | Source code |
| read_alleleFrequencies | Man page Source code |
| read_baf | Man page Source code |
| read_bafsegmented | Man page Source code |
| read_beagle_output | Man page Source code |
| read_gccontent | Man page Source code |
| read_impute_input | Man page Source code |
| read_imputed_output | Man page Source code |
| read_logr | Man page Source code |
| read_replication | Man page Source code |
| read_table_generic | Man page Source code |
| recalc_psi_t | Source code |
| run.beagle5 | Man page Source code |
| run.impute | Man page Source code |
| runASCAT | Source code |
| runFastPcf | Source code |
| runPcfSubset | Source code |
| run_clonal_ASCAT | Source code |
| run_haplotyping | Man page Source code |
| run_haplotyping_germline | Source code |
| runmed_data | Source code |
| segment.baf.phased | Man page Source code |
| segment.baf.phased.legacy | Man page Source code Source code |
| segment.baf.phased.multisample | Man page Source code |
| segment.baf.phased.sv | Man page Source code |
| selectFastPcf | Source code |
| split_genome | Source code |
| split_input_haplotypes | Man page Source code |
| squaresplot | Man page Source code |
| standardiseChrNotation | Source code |
| standardiseChrNotation_germline | Source code |
| studentise | Source code |
| suggest_refit | Man page Source code |
| totalcn_chrom_plot | Man page Source code |
| write_battenberg_phasing | Man page Source code |
| writebeagle.as.impute | Man page Source code |
| writevcf.beagle | Man page Source code |
