Index

A

absolute_clonal() (in module cnvlib.call) absolute_dataframe() (in module cnvlib.call) absolute_expect() (in module cnvlib.call) absolute_pure() (in module cnvlib.call) absolute_reference() (in module cnvlib.call) absolute_threshold() (in module cnvlib.call) add() (cnvlib.gary.GenomicArray method) add_columns() (cnvlib.gary.GenomicArray method)

add_refflat_names() (in module cnvlib.target) apply_weights() (in module cnvlib.fix) as_columns() (cnvlib.gary.GenomicArray method) as_dataframe() (cnvlib.gary.GenomicArray method) as_rows() (cnvlib.gary.GenomicArray method) assert_equal() (in module cnvlib.core) assign_names() (in module cnvlib.target) autosomes() (cnvlib.gary.GenomicArray method)

B

baf_by_ranges() (cnvlib.vary.VariantArray method) bam_total_reads() (in module cnvlib.coverage) batch_make_reference() (in module cnvlib.commands) batch_run_sample() (in module cnvlib.commands) batch_write_coverage() (in module cnvlib.commands) bc_chromosome_draw_label() (in module cnvlib.diagram) bc_organism_draw() (in module cnvlib.diagram)

bed2probes() (in module cnvlib.reference) bedcov() (in module cnvlib.coverage) build_chrom_diagram() (in module cnvlib.diagram) by_chromosome() (cnvlib.gary.GenomicArray method) by_gene() (cnvlib.cnary.CopyNumArray method) by_ranges() (cnvlib.gary.GenomicArray method)

C

calculate_gc_lo() (in module cnvlib.reference) call_quiet() (in module cnvlib.core) center_all() (cnvlib.cnary.CopyNumArray method) center_by_window() (in module cnvlib.fix) check_inputs() (in module cnvlib.smoothing) check_unique() (in module cnvlib.core) chromosome (cnvlib.gary.GenomicArray attribute) chromosome_sizes() (in module cnvlib.plots) cnv_on_chromosome() (in module cnvlib.plots) cnv_on_genome() (in module cnvlib.plots) cnvlib (module) cnvlib.antitarget (module) cnvlib.call (module) cnvlib.cnary (module) cnvlib.commands (module) cnvlib.core (module) cnvlib.coverage (module) cnvlib.diagram (module) cnvlib.export (module) cnvlib.fix (module) cnvlib.gary (module) cnvlib.importers (module)

cnvlib.metrics (module) cnvlib.ngfrills (module) cnvlib.parallel (module) cnvlib.params (module) cnvlib.plots (module) cnvlib.reference (module) cnvlib.reports (module) cnvlib.segmentation (module) cnvlib.smoothing (module) cnvlib.target (module) cnvlib.vary (module) combine_probes() (in module cnvlib.reference) compare_sex_chromosomes() (cnvlib.cnary.CopyNumArray method) concat() (cnvlib.gary.GenomicArray method) confidence_interval_bootstrap() (in module cnvlib.metrics) coords() (cnvlib.gary.GenomicArray method) copy() (cnvlib.gary.GenomicArray method) CopyNumArray (class in cnvlib.cnary) create_chrom_ids() (in module cnvlib.export) create_diagram() (in module cnvlib.diagram) csvstring() (in module cnvlib.commands) cvg2rgb() (in module cnvlib.plots)

D

do_access() (in module cnvlib.commands) do_antitarget() (in module cnvlib.commands) do_breaks() (in module cnvlib.commands) do_call() (in module cnvlib.commands) do_coverage() (in module cnvlib.commands) do_fix() (in module cnvlib.commands) do_gainloss() (in module cnvlib.commands) do_gender() (in module cnvlib.commands) do_heatmap() (in module cnvlib.commands) do_import_theta() (in module cnvlib.commands)

do_metrics() (in module cnvlib.commands) do_reference() (in module cnvlib.commands) do_reference_flat() (in module cnvlib.commands) do_scatter() (in module cnvlib.commands) do_segmentation() (in module cnvlib.segmentation) do_targets() (in module cnvlib.commands) drop_extra_columns() (cnvlib.gary.GenomicArray method) drop_low_coverage() (cnvlib.cnary.CopyNumArray method) drop_outliers() (in module cnvlib.segmentation)

E

edge_gains() (in module cnvlib.fix) edge_losses() (in module cnvlib.fix) emit() (in module cnvlib.target) end (cnvlib.gary.GenomicArray attribute) ensure_path() (in module cnvlib.core) ests_of_scale() (in module cnvlib.metrics) expect_flat_log2() (cnvlib.cnary.CopyNumArray method)

export_bed() (in module cnvlib.export) export_nexus_basic() (in module cnvlib.export) export_nexus_ogt() (in module cnvlib.export) export_seg() (in module cnvlib.export) export_theta() (in module cnvlib.export) export_theta_snps() (in module cnvlib.export) export_vcf() (in module cnvlib.export)

F

fbase() (in module cnvlib.core) filter_names() (in module cnvlib.target) find_background_regions() (in module cnvlib.antitarget) find_picard_files() (in module cnvlib.importers) fit_edges() (in module cnvlib.smoothing)

fmt_cdt() (in module cnvlib.export) fmt_gct() (in module cnvlib.export) fmt_jtv() (in module cnvlib.export) from_columns() (cnvlib.gary.GenomicArray class method) from_rows() (cnvlib.gary.GenomicArray class method)

G

gainloss_by_gene() (in module cnvlib.reports) gainloss_by_segment() (in module cnvlib.reports) gene_coords_by_name() (in module cnvlib.plots) gene_coords_by_range() (in module cnvlib.plots) GenomicArray (class in cnvlib.gary) get_background() (in module cnvlib.antitarget) get_breakpoints() (in module cnvlib.reports)

get_edge_bias() (in module cnvlib.fix) get_fasta_stats() (in module cnvlib.reference) get_gene_intervals() (in module cnvlib.reports) group_by_genes() (in module cnvlib.reports) group_snvs_by_segments() (in module cnvlib.plots) guess_chromosome_regions() (in module cnvlib.antitarget) guess_xx() (cnvlib.cnary.CopyNumArray method)

H

heterozygous() (cnvlib.vary.VariantArray method)

I

in_range() (cnvlib.gary.GenomicArray method) in_ranges() (cnvlib.gary.GenomicArray method) interval_coverages() (in module cnvlib.coverage)

interval_coverages_count() (in module cnvlib.coverage) interval_coverages_pileup() (in module cnvlib.coverage)

K

keep_columns() (cnvlib.gary.GenomicArray method)

L

labels() (cnvlib.gary.GenomicArray method) load_adjust_coverages() (in module cnvlib.fix)

log2 (cnvlib.cnary.CopyNumArray attribute) log2_ratios() (in module cnvlib.call)

M

map() (cnvlib.parallel.SerialPool method) mask_bad_bins() (in module cnvlib.fix) match_ref_to_sample() (in module cnvlib.fix)

match_to_bins() (cnvlib.gary.GenomicArray method) merge_samples() (in module cnvlib.export) mirrored_baf() (cnvlib.vary.VariantArray method)

O

outlier_iqr() (in module cnvlib.smoothing)

outlier_mad_median() (in module cnvlib.smoothing)

P

parse_args() (in module cnvlib.commands) parse_range_text() (in module cnvlib.plots) parse_refflat_line() (in module cnvlib.target) parse_theta_results() (in module cnvlib.importers) partition_by_chrom() (in module cnvlib.plots)

pick_pool() (in module cnvlib.parallel) plot_x_dividers() (in module cnvlib.plots) prediction_interval() (in module cnvlib.metrics) print_version() (in module cnvlib.commands)

R

rbase() (in module cnvlib.core) read() (in module cnvlib) read_refflat_genes() (in module cnvlib.target) ref_means_nbins() (in module cnvlib.export) reference2regions() (in module cnvlib.reference) region_depth_count() (in module cnvlib.coverage) repair_segments() (in module cnvlib.segmentation) rescale_baf() (in module cnvlib.call) residuals() (cnvlib.cnary.CopyNumArray method)

result() (cnvlib.parallel.SerialFuture method) rm() (in module cnvlib.coverage) rolling_median() (in module cnvlib.smoothing) rolling_outlier_iqr() (in module cnvlib.smoothing) rolling_outlier_quantile() (in module cnvlib.smoothing) rolling_outlier_std() (in module cnvlib.smoothing) rolling_quantile() (in module cnvlib.smoothing) rolling_std() (in module cnvlib.smoothing) row2label() (cnvlib.gary.GenomicArray static method)

S

safe_write() (in module cnvlib.core) sample_id (cnvlib.gary.GenomicArray attribute) segment_mean() (in module cnvlib.metrics) segments2vcf() (in module cnvlib.export) select() (cnvlib.gary.GenomicArray method) SerialFuture (class in cnvlib.parallel) SerialPool (class in cnvlib.parallel) setup_chromosome() (in module cnvlib.plots) setup_genome() (in module cnvlib.plots) shift_xx() (cnvlib.cnary.CopyNumArray method) shorten_labels() (in module cnvlib.target) shortest_name() (in module cnvlib.target) shuffle() (cnvlib.gary.GenomicArray method)

shutdown() (cnvlib.parallel.SerialPool method) smoothed() (in module cnvlib.smoothing) snv_on_chromosome() (in module cnvlib.plots) snv_on_genome() (in module cnvlib.plots) sort() (cnvlib.gary.GenomicArray method) sort_columns() (cnvlib.gary.GenomicArray method) sorter_chrom() (in module cnvlib.core) sorter_chrom_at() (in module cnvlib.core) split_targets() (in module cnvlib.target) squash_genes() (cnvlib.cnary.CopyNumArray method) squash_segments() (in module cnvlib.segmentation) start (cnvlib.gary.GenomicArray attribute) submit() (cnvlib.parallel.SerialPool method)

T

temp_write_text() (in module cnvlib.core) test_loh() (in module cnvlib.plots) theta_read_counts() (in module cnvlib.export)

to_chunks() (in module cnvlib.coverage) transfer_fields() (in module cnvlib.segmentation) tumor_boost() (cnvlib.vary.VariantArray method)

U

unpack_range() (in module cnvlib.plots)

V

VariantArray (class in cnvlib.vary)

verify_gender_arg() (in module cnvlib.commands)

W

warn_bad_probes() (in module cnvlib.reference) write_dataframe() (in module cnvlib.core)

write_text() (in module cnvlib.core) write_tsv() (in module cnvlib.core)

Z

zip_repeater() (in module cnvlib.commands)