Index

_

__init__() (pylluminator.annotations.Annotations method) (pylluminator.annotations.ArrayType method) (pylluminator.annotations.Channel method) (pylluminator.annotations.GenomeInfo method) (pylluminator.annotations.GenomeVersion method) (pylluminator.dm.DM method) (pylluminator.dm.DM_TYPE method) (pylluminator.mask.Mask method) (pylluminator.mask.MaskCollection method) (pylluminator.read_idat.IdatDataset method) (pylluminator.read_idat.IdatHeaderLocation method) (pylluminator.read_idat.IdatSectionCode method) (pylluminator.samples.Samples method)

A

add_annotation_info() (pylluminator.samples.Samples method) add_mask() (pylluminator.mask.MaskCollection method) analyze_replicates() (in module pylluminator.visualizations)

Annotations (class in pylluminator.annotations) ArrayType (class in pylluminator.annotations) as_integer_ratio() (pylluminator.read_idat.IdatHeaderLocation method) (pylluminator.read_idat.IdatSectionCode method)

B

background_correction_noob_fit() (in module pylluminator.stats) batch_correction() (pylluminator.samples.Samples method) betas_2D() (in module pylluminator.visualizations) betas_dendrogram() (in module pylluminator.visualizations) betas_density() (in module pylluminator.visualizations) betas_heatmap() (in module pylluminator.visualizations)

betas_stats() (in module pylluminator.quality_control) bit_count() (pylluminator.read_idat.IdatHeaderLocation method) (pylluminator.read_idat.IdatSectionCode method) bit_length() (pylluminator.read_idat.IdatHeaderLocation method) (pylluminator.read_idat.IdatSectionCode method) bytes_to_int() (in module pylluminator.read_idat)

C

calculate_betas() (pylluminator.samples.Samples method) cg_probes() (pylluminator.samples.Samples method) ch_probes() (pylluminator.samples.Samples method) Channel (class in pylluminator.annotations) cns_manhattan_plot() (in module pylluminator.visualizations) column_names_to_snake_case() (in module pylluminator.utils) combine_p_values_stouffer() (in module pylluminator.dm) compute_dmp() (pylluminator.dm.DM method) compute_dmr() (pylluminator.dm.DM method) concatenate_non_na() (in module pylluminator.utils) conjugate() (pylluminator.read_idat.IdatHeaderLocation method) (pylluminator.read_idat.IdatSectionCode method)

controls() (pylluminator.samples.Samples method) convert_to_path() (in module pylluminator.utils) copy() (pylluminator.annotations.Annotations method) (pylluminator.annotations.GenomeInfo method) (pylluminator.mask.Mask method) (pylluminator.mask.MaskCollection method) (pylluminator.samples.Samples method) copy_number_segmentation() (in module pylluminator.cnv) copy_number_variation() (in module pylluminator.cnv) create_from_idats() (in module pylluminator.sample_sheet)

D

denominator (pylluminator.read_idat.IdatHeaderLocation attribute) (pylluminator.read_idat.IdatSectionCode attribute) detect_array() (in module pylluminator.annotations) detection_stats() (in module pylluminator.quality_control) DM (class in pylluminator.dm) DM_TYPE (class in pylluminator.dm) dmp_heatmap() (in module pylluminator.visualizations)

dmr_manhattan_plot() (in module pylluminator.visualizations) download_from_geo() (in module pylluminator.utils) download_from_link() (in module pylluminator.utils) drop_samples() (pylluminator.samples.Samples method) dye_bias_correction() (pylluminator.samples.Samples method) dye_bias_correction_l() (pylluminator.samples.Samples method) dye_bias_correction_nl() (pylluminator.samples.Samples method) dye_bias_stats() (in module pylluminator.quality_control)

F

from_bytes() (pylluminator.read_idat.IdatHeaderLocation method) (pylluminator.read_idat.IdatSectionCode method)

from_sesame() (in module pylluminator.samples)

G

GenomeInfo (class in pylluminator.annotations) GenomeVersion (class in pylluminator.annotations) get_betas() (pylluminator.samples.Samples method) get_chromosome_number() (in module pylluminator.utils) get_column_as_flat_array() (in module pylluminator.utils) get_factors_from_formula() (in module pylluminator.stats) get_file_object() (in module pylluminator.read_idat) get_files_matching() (in module pylluminator.utils) get_logger() (in module pylluminator.utils) get_logger_level() (in module pylluminator.utils) get_m_values() (pylluminator.samples.Samples method) get_mask() (pylluminator.mask.MaskCollection method) get_mask_names() (pylluminator.mask.MaskCollection method)

get_mean_ib_intensity() (pylluminator.samples.Samples method) get_nb_probes_per_chr_and_type() (pylluminator.samples.Samples method) get_negative_controls() (pylluminator.samples.Samples method) get_normalization_controls() (pylluminator.samples.Samples method) get_normalization_samples() (in module pylluminator.cnv) get_or_download_annotation_data() (in module pylluminator.annotations) get_probes() (pylluminator.samples.Samples method) get_probes_with_probe_type() (pylluminator.samples.Samples method) get_resource_folder() (in module pylluminator.utils) get_signal_df() (pylluminator.samples.Samples method) get_top() (pylluminator.dm.DM method) get_total_ib_intensity() (pylluminator.samples.Samples method) GREEN (pylluminator.annotations.Channel attribute)

H

has_betas() (pylluminator.samples.Samples method) HG19 (pylluminator.annotations.GenomeVersion attribute) HG38 (pylluminator.annotations.GenomeVersion attribute) huber() (in module pylluminator.stats) HUMAN_27K (pylluminator.annotations.ArrayType attribute)

HUMAN_450K (pylluminator.annotations.ArrayType attribute) HUMAN_EPIC (pylluminator.annotations.ArrayType attribute) HUMAN_EPIC_PLUS (pylluminator.annotations.ArrayType attribute) HUMAN_EPIC_V2 (pylluminator.annotations.ArrayType attribute) HUMAN_MSA (pylluminator.annotations.ArrayType attribute)

I

ib() (pylluminator.samples.Samples method) ib_green() (pylluminator.samples.Samples method) ib_red() (pylluminator.samples.Samples method) IdatDataset (class in pylluminator.read_idat) IdatHeaderLocation (class in pylluminator.read_idat) IdatSectionCode (class in pylluminator.read_idat) imag (pylluminator.read_idat.IdatHeaderLocation attribute) (pylluminator.read_idat.IdatSectionCode attribute)

infer_type1_channel() (pylluminator.samples.Samples method) intensity_stats() (in module pylluminator.quality_control) iqr() (in module pylluminator.stats) is_green (pylluminator.annotations.Channel property) is_human() (pylluminator.annotations.ArrayType method) (pylluminator.annotations.GenomeVersion method) is_integer() (pylluminator.read_idat.IdatHeaderLocation method) (pylluminator.read_idat.IdatSectionCode method) is_red (pylluminator.annotations.Channel property)

L

load() (pylluminator.samples.Samples static method)

load_object() (in module pylluminator.utils)

M

make_genomic_ranges() (pylluminator.annotations.Annotations method) MAMMAL_40 (pylluminator.annotations.ArrayType attribute) Mask (class in pylluminator.mask) mask_control_probes() (pylluminator.samples.Samples method) mask_non_cg_probes() (pylluminator.samples.Samples method) mask_non_unique_probes() (pylluminator.samples.Samples method) mask_probes_by_names() (pylluminator.samples.Samples method) mask_quality_probes() (pylluminator.samples.Samples method) mask_snp_probes() (pylluminator.samples.Samples method) mask_xy_probes() (pylluminator.samples.Samples method) MaskCollection (class in pylluminator.mask) merge_alt_chromosomes() (in module pylluminator.utils) merge_samples_by() (pylluminator.samples.Samples method) merge_series_values() (in module pylluminator.utils) metadata_correlation() (in module pylluminator.visualizations) metadata_pairplot() (in module pylluminator.visualizations)

meth() (pylluminator.samples.Samples method) methylation_distribution() (in module pylluminator.visualizations) MM10 (pylluminator.annotations.GenomeVersion attribute) MM39 (pylluminator.annotations.GenomeVersion attribute) module pylluminator.annotations pylluminator.cnv pylluminator.dm pylluminator.mask pylluminator.quality_control pylluminator.read_idat pylluminator.sample_sheet pylluminator.samples pylluminator.stats pylluminator.utils pylluminator.visualizations MOUSE_MM285 (pylluminator.annotations.ArrayType attribute)

N

nb_probes (pylluminator.samples.Samples property) nb_probes_per_chr_and_type_hist() (in module pylluminator.visualizations) nb_probes_stats() (in module pylluminator.quality_control) nb_samples (pylluminator.samples.Samples property) non_unique_mask_names (pylluminator.annotations.Annotations property)

noob_background_correction() (pylluminator.samples.Samples method) norm_exp_convolution() (in module pylluminator.stats) npread() (in module pylluminator.read_idat) number_probes_masked() (pylluminator.mask.MaskCollection method) numerator (pylluminator.read_idat.IdatHeaderLocation attribute) (pylluminator.read_idat.IdatSectionCode attribute)

O

oob() (pylluminator.samples.Samples method) oob_green() (pylluminator.samples.Samples method)

oob_red() (pylluminator.samples.Samples method) overflow_check() (pylluminator.read_idat.IdatDataset method)

P

pc_association_heatmap() (in module pylluminator.visualizations) pc_correlation_heatmap() (in module pylluminator.visualizations) poobah() (pylluminator.samples.Samples method) probe_ids (pylluminator.samples.Samples property) pylluminator.annotations module pylluminator.cnv module pylluminator.dm module pylluminator.mask module pylluminator.quality_control module

pylluminator.read_idat module pylluminator.sample_sheet module pylluminator.samples module pylluminator.stats module pylluminator.utils module pylluminator.visualizations module

Q

quality_mask_names (pylluminator.annotations.Annotations property)

quantile_normalization_using_target() (in module pylluminator.stats)

R

read() (pylluminator.read_idat.IdatDataset method) read_and_reset() (in module pylluminator.read_idat) read_byte() (in module pylluminator.read_idat) read_char() (in module pylluminator.read_idat) read_from_file() (in module pylluminator.sample_sheet) read_idata() (in module pylluminator.samples) read_int() (in module pylluminator.read_idat) read_long() (in module pylluminator.read_idat) read_samples() (in module pylluminator.samples) read_short() (in module pylluminator.read_idat)

read_string() (in module pylluminator.read_idat) real (pylluminator.read_idat.IdatHeaderLocation attribute) (pylluminator.read_idat.IdatSectionCode attribute) RED (pylluminator.annotations.Channel attribute) remove_masks() (pylluminator.mask.MaskCollection method) remove_probe_suffix() (in module pylluminator.utils) remove_probes_suffix() (pylluminator.samples.Samples method) reset_betas() (pylluminator.samples.Samples method) reset_masks() (pylluminator.mask.MaskCollection method) reset_poobah() (pylluminator.samples.Samples method)

S

sample_label_name (pylluminator.samples.Samples property) sample_labels (pylluminator.samples.Samples property) Samples (class in pylluminator.samples) save() (pylluminator.samples.Samples method) save_object() (in module pylluminator.utils) scrub_background_correction() (pylluminator.samples.Samples method)

select_dmps() (pylluminator.dm.DM method) set_channel_index_as() (in module pylluminator.utils) set_level_as_index() (in module pylluminator.utils) set_logger() (in module pylluminator.utils) show_chromosome_legend() (in module pylluminator.visualizations) snp_probes() (pylluminator.samples.Samples method) subset() (pylluminator.samples.Samples method)

T

to_bytes() (pylluminator.read_idat.IdatHeaderLocation method) (pylluminator.read_idat.IdatSectionCode method) type1() (pylluminator.samples.Samples method)

type1_color_channels_stats() (in module pylluminator.quality_control) type1_green() (pylluminator.samples.Samples method) type1_red() (pylluminator.samples.Samples method) type2() (pylluminator.samples.Samples method)

U

unmeth() (pylluminator.samples.Samples method)

V

visualize_gene() (in module pylluminator.visualizations)