Man pages for Wedge-Oxford/battenberg
Battenberg subclonal copy number caller
| allele_ratio_plot | Plot allele ratios from raw segmented data |
| battenberg | Run the Battenberg pipeline |
| calc_rho_psi_refit | Calculate rho and psi values from a refit suggestion |
| callChrXsubclones | Fit ChrX subclonal copy number (male only) |
| call_multisample_MSAI | Generates haplotype blocks, MSAI results, and plots from... |
| callSubclones | Fit subclonal copy number |
| cel2baf.logr | Transform cel files into BAF and LogR |
| check.imputeinfofile | Check impute info file consistency |
| cnfit_to_refit_suggestions | Create refit suggestions for a fit copy number profile |
| combine.baf.files | Combines all separate BAF files per chromosome into a single... |
| combine.impute.output | Concatenate the impute output generated for each of the... |
| convert.impute.input.to.beagle.input | Converts impute input to a beagle input |
| coverage_plot | Plot relative coverage of tumour and normal |
| fit.copy.number | Fit copy number |
| gc.correct | Correct the LogR estimates for GC content |
| gc.correct.wgs | Function to correct LogR for waivyness that correlates with... |
| generate.impute.input.snp6 | Prepares data for impute |
| generate.impute.input.wgs | Prepare data for impute |
| getAlleleCounts | Obtain allele counts for 1000 Genomes loci through external... |
| getBAFsAndLogRs | Obtain BAF and LogR from the allele counts |
| get.chrom.names | Returns the chromosome names that are supported |
| GetChromosomeBAFs | Morphs phased SNPs from WGS input into haplotype blocks |
| GetChromosomeBAFs_SNP6 | Morphs phased SNPs from SNP6 input into haplotype blocks |
| get_multisample_phasing | Generates phased haplotypes from multisample Battenberg runs |
| infer_gender_birdseed | Infer the gender using the birdseed report file |
| input_known_haplotypes | Combine imputation results with external haplotype blocks |
| make_posthoc_plots | Function to make additional figures |
| mask_high_cn_segments | Mask segments that have a too high CN state |
| parse.imputeinfofile | Read in the imputeinfofile. |
| plot.haplotype.data | Plot haplotyped SNPs |
| prepare_snp6 | Prepare SNP6 data for haplotype construction |
| prepare_wgs | Prepare WGS data for haplotype construction |
| read_alleleFrequencies | Parser for allele frequencies data |
| read_baf | Parser for BAF data |
| read_bafsegmented | Parser for BAFsegmented data |
| read_beagle_output | Parser for beagle5 output data |
| read_gccontent | Parser for GC content reference data |
| read_imputed_output | Parser for imputed genotype data |
| read_impute_input | Parser for impute input data |
| read_logr | Parser for logR data |
| read_replication | Parser for replication timing reference data |
| read_table_generic | Generic reading function using the readr R package, tailored... |
| run.beagle5 | Command to run beagle5 |
| run_haplotyping | Construct haplotypes for a chromosome |
| run.impute | Run impute on the specified inputfile |
| segment.baf.phased | Segment BAF, with the possible inclusion of structural... |
| segment.baf.phased.legacy | Segment the haplotyped and phased data using fastPCF. This is... |
| segment.baf.phased.multisample | Segment BAF, with the possible inclusion of structural... |
| segment.baf.phased.sv | Segment BAF with the inclusion of structural variant... |
| split_input_haplotypes | Split a single vcf into separate vcfs for each chromosome |
| squaresplot | Plot Battenberg copy number solutions for a segment |
| suggest_refit | Calculate refit values from a refit suggestion |
| totalcn_chrom_plot | Plot total copy number split per chromosome |
| write_battenberg_phasing | Writes the imputation and copy number phased haplotypes to a... |
| writebeagle.as.impute | Writes output of beagle as output from impute (interface... |
| writevcf.beagle | Writes input file for beagle5 |
