Index

_

__init__() (methylcheck.reports.qc_report.ReportPDF method)

A

assign() (in module methylcheck) (in module methylcheck.samples)

B

beta_density_plot() (in module methylcheck) (in module methylcheck.samples)

beta_mds_plot() (in module methylcheck) (in module methylcheck.samples) bis_conversion_control() (in module methylcheck.qc_plot)

C

combine_mds() (in module methylcheck) (in module methylcheck.samples)

container_to_pkl() (in module methylcheck.load_processed) cumulative_sum_beta_distribution() (in module methylcheck) (in module methylcheck.samples)

D

detect_header_pattern() (in module methylcheck.read_geo_processed)

drop_nan_probes() (in module methylcheck) (in module methylcheck.probes)

E

exclude_probes() (in module methylcheck) (in module methylcheck.probes)

exclude_sex_control_probes() (in module methylcheck) (in module methylcheck.probes) exec_summary() (methylcheck.reports.qc_report.ReportPDF method)

G

get_sex() (in module methylcheck) (in module methylcheck.predict)

I

infer_strain() (in module methylcheck.predict)

L

list_problem_probes() (in module methylcheck) (in module methylcheck.probes) load() (in module methylcheck) (in module methylcheck.load_processed)

load_both() (in module methylcheck) (in module methylcheck.load_processed)

M

mean_beta_compare() (in module methylcheck) (in module methylcheck.samples) mean_beta_plot() (in module methylcheck) (in module methylcheck.samples) methylcheck.cli (module) methylcheck.load_processed (module)

methylcheck.predict (module), [1] methylcheck.probes (module), [1] methylcheck.qc_plot (module) methylcheck.read_geo_processed (module) methylcheck.reports.qc_report.run_pipeline (module) methylcheck.samples (module), [1]

O

open_error_buffer() (methylcheck.reports.qc_report.ReportPDF method)

P

page_of_paragraphs() (methylcheck.reports.qc_report.ReportPDF method) page_of_text() (methylcheck.reports.qc_report.ReportPDF method) parse_custom_tables() (methylcheck.reports.qc_report.ReportPDF method) plot_assigned_groups() (in module methylcheck.samples) plot_beta_by_type() (in module methylcheck) (in module methylcheck.qc_plot)

plot_controls() (in module methylcheck) (in module methylcheck.qc_plot) plot_M_vs_U() (in module methylcheck) (in module methylcheck.qc_plot) problem_probe_reasons() (in module methylcheck.probes)

Q

qc_signal_intensity() (in module methylcheck) (in module methylcheck.qc_plot)

R

read_geo() (in module methylcheck) (in module methylcheck.read_geo_processed) ReportPDF (class in methylcheck.reports.qc_report)

run_pipeline() (in module methylcheck) run_qc() (in module methylcheck) (in module methylcheck.qc_plot)

S

sample_plot() (in module methylcheck) (in module methylcheck.samples)

T

to_table() (methylcheck.reports.qc_report.ReportPDF method)