Man pages for Wedge-Oxford/battenberg
Battenberg subclonal copy number caller

allele_ratio_plotPlot allele ratios from raw segmented data
battenbergRun the Battenberg pipeline
calc_psi_tCalculate psi based on a reference segment and its associated...
calc_rho_psi_refitCalculate rho and psi values from a refit suggestion
callSubclonesFit subclonal copy number
cel2baf.logrTransform cel files into BAF and LogR
cnfit_to_refit_suggestionsCreate refit suggestions for a fit copy number profile
combine.baf.filesCombines all separate BAF files per chromosome into a single...
combine.impute.outputConcatenate the impute output generated for each of the...
coverage_plotPlot relative coverage of tumour and normal
find_centroid_of_global_minimaThis function is an alternative procedure for finding the...
fit.copy.numberFit copy number
gc.correctCorrect the LogR estimates for GC content
gc.correct.wgsFunction to correct LogR for waivyness that correlates with...
generate.impute.input.snp6Prepares data for impute
generate.impute.input.wgsPrepare data for impute
getAlleleCountsObtain allele counts for 1000 Genomes loci through external...
getBAFsAndLogRsObtain BAF and LogR from the allele counts
get.chrom.namesReturns the chromosome names that are supported
GetChromosomeBAFsMorphs phased SNPs from WGS input into haplotype blocks
GetChromosomeBAFs_SNP6Morphs phased SNPs from SNP6 input into haplotype blocks
infer_gender_birdseedInfer the gender using the birdseed report file
make_posthoc_plotsFunction to make additional figures
mask_high_cn_segmentsMask segments that have a too high CN state
parse.imputeinfofileRead in the imputeinfofile.
plot.haplotype.dataPlot haplotyped SNPs
prepare_snp6Prepare SNP6 data for haplotype construction
prepare_wgsPrepare WGS data for haplotype construction
read_table_genericGeneric reading function using the readr R package, tailored...
runASCATA modified ASCAT main function to fit Battenberg
run_clonal_ASCATASCAT like function to obtain a clonal copy number profile
run_haplotypingConstruct haplotypes for a chromosome
run.imputeRun impute on the specified inputfile
segment.baf.phasedSegment the haplotyped and phased data using fastPCF.
segment.baf.phased.svSegment BAF with the inclusion of structural variant...
squaresplotPlot Battenberg copy number solutions for a segment
suggest_refitCalculate refit values from a refit suggestion
totalcn_chrom_plotPlot total copy number split per chromosome
Wedge-Oxford/battenberg documentation built on March 20, 2018, 7:49 p.m.