Index

A

apply_async() (cnvlib.commands.SerialPool method) apply_weights() (in module cnvlib.fix)

assert_equal() (in module cnvlib.core)

B

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)

biweight_location() (in module cnvlib.metrics) biweight_midvariance() (in module cnvlib.metrics) build_chrom_diagram() (in module cnvlib.diagram) by_bin() (cnvlib.cnarray.CopyNumArray method) by_chromosome() (cnvlib.cnarray.CopyNumArray method) by_gene() (cnvlib.cnarray.CopyNumArray method) by_segment() (cnvlib.cnarray.CopyNumArray method)

C

calculate_gc_lo() (in module cnvlib.reference) calculate_theta_fields() (in module cnvlib.export) call_quiet() (in module cnvlib.ngfrills) center_all() (cnvlib.cnarray.CopyNumArray method) center_by_window() (in module cnvlib.fix) check_inputs() (in module cnvlib.smoothing) check_unique() (in module cnvlib.core) chrom (cnvlib.export.ProbeInfo attribute) chromosome (cnvlib.cnarray.CopyNumArray attribute) chromosome_sizes() (in module cnvlib.plots) close() (cnvlib.commands.SerialPool method) cna_absolutes() (in module cnvlib.export) cnvlib (module) cnvlib.antitarget (module) cnvlib.cnarray (module) cnvlib.commands (module) cnvlib.core (module) cnvlib.coverage (module) cnvlib.diagram (module) cnvlib.export (module)

cnvlib.fix (module) cnvlib.importers (module) cnvlib.metrics (module) cnvlib.ngfrills (module) cnvlib.params (module) cnvlib.plots (module) cnvlib.reference (module) cnvlib.reports (module) cnvlib.segmentation (module) cnvlib.smoothing (module) combine_probes() (in module cnvlib.reference) copy() (cnvlib.cnarray.CopyNumArray method) CopyNumArray (class in cnvlib.cnarray) coverage (cnvlib.cnarray.CopyNumArray attribute) create_chrom_ids() (in module cnvlib.export) create_diagram() (in module cnvlib.diagram) create_heatmap() (in module cnvlib.commands) create_loh() (in module cnvlib.commands) cvg2rgb() (in module cnvlib.plots)

D

do_antitarget() (in module cnvlib.commands) do_breaks() (in module cnvlib.commands) do_coverage() (in module cnvlib.commands) do_fix() (in module cnvlib.commands) do_gainloss() (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.cnarray.CopyNumArray method)

E

echo() (in module cnvlib.ngfrills) edge_gain() (in module cnvlib.fix) edge_loss() (in module cnvlib.fix) end (cnvlib.cnarray.CopyNumArray attribute) (cnvlib.export.ProbeInfo attribute) ensure_bam_index() (in module cnvlib.ngfrills) ensure_bam_sorted() (in module cnvlib.ngfrills) ensure_fasta_index() (in module cnvlib.ngfrills)

ensure_path() (in module cnvlib.ngfrills) ests_of_scale() (in module cnvlib.metrics) export_freebayes() (in module cnvlib.export) export_nexus_basic() (in module cnvlib.export) export_seg() (in module cnvlib.export) export_theta() (in module cnvlib.export) extend() (cnvlib.cnarray.CopyNumArray method)

F

fasta_extract_regions() (in module cnvlib.ngfrills) fbase() (in module cnvlib.core) filter_column() (in module cnvlib.coverage) filter_read() (in module cnvlib.coverage) filter_vcf_lines() (in module cnvlib.ngfrills) 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) fmt_multi() (in module cnvlib.export) fmt_vcf() (in module cnvlib.export) from_rows() (cnvlib.cnarray.CopyNumArray class method)

G

gene (cnvlib.cnarray.CopyNumArray attribute) (cnvlib.export.ProbeInfo attribute) gene_coords_by_name() (in module cnvlib.plots) gene_coords_by_range() (in module cnvlib.plots) get_background() (in module cnvlib.antitarget) get_breakpoints() (in module cnvlib.reports) get_fasta_stats() (in module cnvlib.reference) get_gene_intervals() (in module cnvlib.reports)

get_relative_chrx_cvg() (in module cnvlib.core) group_bed_tracks() (in module cnvlib.ngfrills) group_by_genes() (in module cnvlib.reports) group_coords() (in module cnvlib.antitarget) guess_chr_x() (in module cnvlib.core) guess_chromosome_regions() (in module cnvlib.antitarget) guess_xx() (in module cnvlib.core)

I

import_seg() (in module cnvlib.importers) in_range() (cnvlib.cnarray.CopyNumArray method) interquartile_range() (in module cnvlib.metrics) interval_coverages() (in module cnvlib.coverage)

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

J

join() (cnvlib.commands.SerialPool method)

L

label (cnvlib.export.ProbeInfo attribute) labels() (cnvlib.cnarray.CopyNumArray method) limit() (in module cnvlib.plots)

load_adjust_coverages() (in module cnvlib.fix) load_targetcoverage_csv() (in module cnvlib.importers) load_vcf() (in module cnvlib.ngfrills)

M

make_edge_sorter() (in module cnvlib.fix) mask_bad_probes() (in module cnvlib.reference) match_ref_to_probes() (in module cnvlib.fix)

median_absolute_deviation() (in module cnvlib.metrics) merge_rows() (in module cnvlib.export) merge_samples() (in module cnvlib.export)

O

outlier_iqr() (in module cnvlib.smoothing)

outlier_mad_median() (in module cnvlib.smoothing)

P

parse_args() (in module cnvlib.commands) parse_bed() (in module cnvlib.ngfrills) parse_bed_track() (in module cnvlib.ngfrills) parse_interval_list() (in module cnvlib.ngfrills) parse_range() (in module cnvlib.plots) parse_regions() (in module cnvlib.ngfrills) parse_text_coords() (in module cnvlib.ngfrills) parse_theta_results() (in module cnvlib.importers) parse_tsv() (in module cnvlib.core)

partition_by_chrom() (in module cnvlib.plots) pick_pool() (in module cnvlib.commands) plot_chromosome() (in module cnvlib.plots) plot_genome() (in module cnvlib.plots) plot_loh() (in module cnvlib.plots) plot_x_dividers() (in module cnvlib.plots) probe_center() (in module cnvlib.plots) probe_deviations_from_segments() (in module cnvlib.metrics) ProbeInfo (class in cnvlib.export)

Q

q_n() (in module cnvlib.metrics)

R

rbase() (in module cnvlib.core) read() (cnvlib.cnarray.CopyNumArray class method) (in module cnvlib) read_fasta_index() (in module cnvlib.ngfrills) reference2regions() (in module cnvlib.reference) region_depth_count() (in module cnvlib.coverage) report_bad_line() (in module cnvlib.ngfrills)

rescale_copy_ratios() (in module cnvlib.export) rolling_median() (in module cnvlib.smoothing) round_to_integer() (in module cnvlib.export) row2label() (in module cnvlib.cnarray) row_to_probe_coverage() (in module cnvlib.export)

S

safe_write() (in module cnvlib.ngfrills) segments2freebayes() (in module cnvlib.export) select() (cnvlib.cnarray.CopyNumArray method) SerialPool (class in cnvlib.commands) shift_xx() (in module cnvlib.core) shuffle() (cnvlib.cnarray.CopyNumArray method) smooth_genome_coverages() (in module cnvlib.smoothing) smoothed() (in module cnvlib.smoothing)

sniff_num_columns() (in module cnvlib.ngfrills) sniff_region_format() (in module cnvlib.ngfrills) sort() (cnvlib.cnarray.CopyNumArray method) sorter_chrom() (in module cnvlib.core) sorter_chrom_at() (in module cnvlib.core) squash_genes() (cnvlib.cnarray.CopyNumArray method) squash_segments() (in module cnvlib.segmentation) start (cnvlib.cnarray.CopyNumArray attribute) (cnvlib.export.ProbeInfo attribute)

T

temp_write_text() (in module cnvlib.ngfrills) test_loh() (in module cnvlib.plots)

to_rows() (cnvlib.cnarray.CopyNumArray method)

U

unpipe_name() (in module cnvlib.importers)

W

warn_bad_probes() (in module cnvlib.reference) write() (cnvlib.cnarray.CopyNumArray method)

write_tsv() (in module cnvlib.core)