API for Wedge-Oxford/battenberg
Battenberg subclonal copy number caller

Global functions
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 Source code
assert.file.exists 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 Man page 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
callSubclones Man page Source code
cel2baf.logr 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
coverage_plot Man page Source code
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 Man page Source code
fit.copy.number Man page Source code
gc.correct Man page Source code
gc.correct.wgs Man page Source code
generate.impute.input.snp6 Man page Source code
generate.impute.input.wgs Man page 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_new_bounds Source code
get_segment_info Source code
infer_gender_birdseed 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
psi2psit Source code
psit2psi Source code
read_table_generic Man page Source code
recalc_psi_t Source code
run.impute Man page Source code
runASCAT Man page Source code
runFastPcf Source code
runPcfSubset Source code
run_clonal_ASCAT Man page Source code
runmed_data Source code
segment.baf.phased Man page Source code
segment.baf.phased.sv Man page Source code
selectFastPcf Source code
split_genome Source code
squaresplot Man page Source code
studentise Source code
suggest_refit Man page Source code
totalcn_chrom_plot Man page Source code
Wedge-Oxford/battenberg documentation built on Oct. 5, 2017, 2:04 p.m.