Index

_

_grn (mepylome.dtypes.beads.RawData attribute) _methyl_data (mepylome.dtypes.beads.ReferenceMethylData attribute)

_ratio (mepylome.dtypes.cnv.CNV attribute) _red (mepylome.dtypes.beads.RawData attribute)

A

analysis_dir (mepylome.analysis.methyl.MethylAnalysis attribute) (mepylome.analysis.methyl_aux.IdatHandler attribute) analysis_ids (mepylome.analysis.methyl.MethylAnalysis attribute) (mepylome.analysis.methyl_aux.IdatHandler attribute) Annotation (class in mepylome.dtypes.cnv) annotation (mepylome.analysis.methyl.MethylAnalysis attribute) (mepylome.analysis.methyl_aux.IdatHandler attribute) (mepylome.dtypes.cnv.CNV attribute)

annotation_df (mepylome.analysis.methyl_aux.IdatHandler attribute) app (mepylome.analysis.methyl.MethylAnalysis attribute) array_type (mepylome.dtypes.beads.RawData attribute) (mepylome.dtypes.cnv.Annotation attribute)

B

balancing_feature (mepylome.analysis.methyl.MethylAnalysis attribute) betas (mepylome.dtypes.beads.MethylData property) betas_all (mepylome.analysis.methyl.MethylAnalysis attribute) betas_at() (mepylome.dtypes.beads.MethylData method)

betas_dir (mepylome.analysis.methyl.MethylAnalysis attribute) betas_sel (mepylome.analysis.methyl.MethylAnalysis attribute) bin_size (mepylome.dtypes.cnv.Annotation attribute) bins (mepylome.dtypes.cnv.CNV attribute)

C

chromsizes (mepylome.dtypes.cnv.Annotation attribute) classifiers (mepylome.analysis.methyl.MethylAnalysis property) classify() (mepylome.analysis.methyl.MethylAnalysis method) cn_summary() (mepylome.analysis.methyl.MethylAnalysis method) CNV (class in mepylome.dtypes.cnv) cnv_dir (mepylome.analysis.methyl.MethylAnalysis attribute) cnv_id (mepylome.analysis.methyl.MethylAnalysis attribute)

cnv_plot (mepylome.analysis.methyl.MethylAnalysis attribute) coef (mepylome.dtypes.cnv.CNV attribute) compute_umap() (mepylome.analysis.methyl.MethylAnalysis method) control_address() (mepylome.dtypes.manifests.Manifest method) control_data_frame (mepylome.dtypes.manifests.Manifest property) cpg_selection (mepylome.analysis.methyl.MethylAnalysis attribute) cpgs (mepylome.analysis.methyl.MethylAnalysis property)

D

data_frame (mepylome.dtypes.manifests.Manifest property) debug (mepylome.analysis.methyl.MethylAnalysis attribute) default_gaps() (mepylome.dtypes.cnv.Annotation static method)

default_genes() (mepylome.dtypes.cnv.Annotation static method) detail (mepylome.dtypes.cnv.Annotation attribute) (mepylome.dtypes.cnv.CNV attribute) dropdown_id (mepylome.analysis.methyl.MethylAnalysis attribute)

F

feature_matrix (mepylome.analysis.methyl.MethylAnalysis attribute) features() (mepylome.analysis.methyl_aux.IdatHandler method)

fit() (mepylome.dtypes.cnv.CNV method) fit_and_evaluate_clf (class in mepylome.analysis.methyl_clf)

G

gap (mepylome.dtypes.cnv.Annotation attribute) get_app() (mepylome.analysis.methyl.MethylAnalysis method)

get_cnv() (mepylome.analysis.methyl.MethylAnalysis method) grn (mepylome.dtypes.beads.MethylData property) (mepylome.dtypes.beads.RawData property)

H

host (mepylome.analysis.methyl.MethylAnalysis attribute)

I

id_to_path (mepylome.analysis.methyl_aux.IdatHandler attribute) idat_basepaths() (in module mepylome.dtypes.beads) idat_handler (mepylome.analysis.methyl.MethylAnalysis property) idat_paths_from_basenames() (in module mepylome.dtypes.beads) IdatHandler (class in mepylome.analysis.methyl_aux)

IdatParser (class in mepylome.dtypes.idat) ids (mepylome.analysis.methyl.MethylAnalysis attribute) (mepylome.dtypes.beads.RawData attribute) ids_to_highlight (mepylome.analysis.methyl.MethylAnalysis attribute) init_parameters() (mepylome.analysis.methyl_aux.IdatHandler method) is_valid_idat_basepath() (in module mepylome.dtypes.beads)

L

load() (mepylome.dtypes.cnv.Annotation static method) (mepylome.dtypes.manifests.Manifest static method)

load_full_betas (mepylome.analysis.methyl.MethylAnalysis attribute)

M

make_bins() (mepylome.dtypes.cnv.Annotation method) make_cnv_plot() (mepylome.analysis.methyl.MethylAnalysis method) make_umap() (mepylome.analysis.methyl.MethylAnalysis method) make_umap_plot() (mepylome.analysis.methyl.MethylAnalysis method) Manifest (class in mepylome.dtypes.manifests) manifest (mepylome.dtypes.cnv.Annotation attribute) mepylome.analysis.methyl module mepylome.analysis.methyl_aux module mepylome.analysis.methyl_clf module mepylome.dtypes.beads module mepylome.dtypes.cnv module mepylome.dtypes.idat module

mepylome.dtypes.manifests module merge_bins() (mepylome.dtypes.cnv.Annotation method) merge_bins_in_chromosome() (mepylome.dtypes.cnv.Annotation static method) MethylAnalysis (class in mepylome.analysis.methyl) methylated (mepylome.dtypes.beads.MethylData property) methylation_probes (mepylome.dtypes.manifests.Manifest property) MethylData (class in mepylome.dtypes.beads) min_probes_per_bin (mepylome.dtypes.cnv.Annotation attribute) mlh1_report_pages() (mepylome.analysis.methyl.MethylAnalysis method) module mepylome.analysis.methyl mepylome.analysis.methyl_aux mepylome.analysis.methyl_clf mepylome.dtypes.beads mepylome.dtypes.cnv mepylome.dtypes.idat mepylome.dtypes.manifests mvalues (mepylome.dtypes.beads.MethylData property)

N

n_cpgs (mepylome.analysis.methyl.MethylAnalysis attribute) n_jobs_clf (mepylome.analysis.methyl.MethylAnalysis attribute)

n_jobs_cnv (mepylome.analysis.methyl.MethylAnalysis attribute) noise (mepylome.dtypes.cnv.CNV attribute)

O

output_dir (mepylome.analysis.methyl.MethylAnalysis attribute)

overlap (mepylome.analysis.methyl.MethylAnalysis attribute) (mepylome.analysis.methyl_aux.IdatHandler attribute)

P

plot() (mepylome.dtypes.cnv.CNV method) port (mepylome.analysis.methyl.MethylAnalysis attribute) precalculate_cnv (mepylome.analysis.methyl.MethylAnalysis attribute) precompute_cnvs() (mepylome.analysis.methyl.MethylAnalysis method) prep (mepylome.analysis.methyl.MethylAnalysis attribute) preprocess_illumina() (mepylome.dtypes.beads.MethylData method)

preprocess_noob() (mepylome.dtypes.beads.MethylData method) preprocess_raw() (mepylome.dtypes.beads.MethylData method) preprocess_swan() (mepylome.dtypes.beads.MethylData method) probe_info() (mepylome.dtypes.manifests.Manifest method) probes (mepylome.dtypes.beads.RawData attribute) (mepylome.dtypes.cnv.Annotation attribute) (mepylome.dtypes.cnv.CNV attribute)

R

ratio (mepylome.dtypes.cnv.CNV attribute) raw_umap_plot (mepylome.analysis.methyl.MethylAnalysis attribute) RawData (class in mepylome.dtypes.beads) read_umap_plot_from_disk() (mepylome.analysis.methyl.MethylAnalysis method) red (mepylome.dtypes.beads.MethylData property) (mepylome.dtypes.beads.RawData property)

reference (mepylome.dtypes.cnv.CNV attribute) reference_dir (mepylome.analysis.methyl.MethylAnalysis attribute) ReferenceMethylData (class in mepylome.dtypes.beads) run_app() (mepylome.analysis.methyl.MethylAnalysis method)

S

sample (mepylome.dtypes.cnv.CNV attribute) samples_annotated (mepylome.analysis.methyl_aux.IdatHandler attribute) segments (mepylome.dtypes.cnv.CNV attribute) selected_columns (mepylome.analysis.methyl_aux.IdatHandler attribute) set_all() (mepylome.dtypes.cnv.CNV class method)

set_betas() (mepylome.analysis.methyl.MethylAnalysis method) set_bins() (mepylome.dtypes.cnv.CNV method) set_detail() (mepylome.dtypes.cnv.CNV method) set_itensity() (mepylome.dtypes.cnv.CNV method) set_segments() (mepylome.dtypes.cnv.CNV method) snp_data_frame (mepylome.dtypes.manifests.Manifest property)

T

test_dir (mepylome.analysis.methyl.MethylAnalysis attribute) (mepylome.analysis.methyl_aux.IdatHandler attribute)

test_ids (mepylome.analysis.methyl.MethylAnalysis attribute) (mepylome.analysis.methyl_aux.IdatHandler attribute)

U

umap_cpgs (mepylome.analysis.methyl.MethylAnalysis attribute) umap_df (mepylome.analysis.methyl.MethylAnalysis attribute) umap_dir (mepylome.analysis.methyl.MethylAnalysis attribute) umap_parms (mepylome.analysis.methyl.MethylAnalysis attribute)

umap_plot (mepylome.analysis.methyl.MethylAnalysis attribute) umap_plot_path (mepylome.analysis.methyl.MethylAnalysis attribute) unmethylated (mepylome.dtypes.beads.MethylData property) use_gpu (mepylome.analysis.methyl.MethylAnalysis attribute)

W

write() (mepylome.dtypes.cnv.CNV method)