Index

A

address_code (methylprep.models.SigSet attribute) alternate_base_filename (methylprep.models.Sample attribute)

ArrayType (class in methylprep) (class in methylprep.models)

B

build_composite_dataset() (in module methylprep) (in module methylprep.download)

build_meta_data() (methylprep.files.SampleSheet method) build_samples() (methylprep.files.SampleSheet method)

C

Channel (class in methylprep.models) check_for_probe_loss() (methylprep.models.SigSet method) columns (methylprep.Manifest attribute) consolidate_values_for_sheet() (in module methylprep) (in module methylprep.processing) contains_column() (methylprep.files.SampleSheet method)

control_data_frame (methylprep.Manifest attribute) ControlProbe (class in methylprep.models) ControlType (class in methylprep.models) convert_miniml() (in module methylprep) (in module methylprep.download) create_sample_sheet() (in module methylprep.files) CUSTOM (methylprep.ArrayType attribute)

D

data_frame (methylprep.Manifest attribute) detect_and_drop_duplicates() (methylprep.models.SigSet method)

download_default() (methylprep.files.Manifest static method) (methylprep.Manifest static method)

E

export() (methylprep.processing.SampleDataContainer method)

F

find_sample_sheet() (in module methylprep.files)

from_probe_count (methylprep.ArrayType attribute)

G

get_array_type() (in module methylprep.models) get_data_types() (methylprep.Manifest method) get_export_filepath() (methylprep.models.Sample method) get_file_s3() (methylprep.models.Sample method) get_filepath() (methylprep.models.Sample method) get_probe_details() (methylprep.files.Manifest method) (methylprep.Manifest method)

get_sample() (methylprep.files.SampleSheet method) get_sample_sheet() (in module methylprep) (in module methylprep.files) get_sample_sheet_s3() (in module methylprep.files) get_samples() (methylprep.files.SampleSheet method)

I

IdatDataset (class in methylprep.files) ILLUMINA_27K (methylprep.ArrayType attribute) ILLUMINA_450K (methylprep.ArrayType attribute)

ILLUMINA_EPIC (methylprep.ArrayType attribute) ILLUMINA_EPIC_PLUS (methylprep.ArrayType attribute) ILLUMINA_MOUSE (methylprep.ArrayType attribute)

M

make_pipeline() (in module methylprep) Manifest (class in methylprep) (class in methylprep.files) meta() (methylprep.files.IdatDataset method) methylprep (module)

methylprep.download (module) methylprep.files (module) methylprep.models (module) methylprep.processing (module) mouse_data_frame (methylprep.Manifest attribute)

N

num_controls (methylprep.ArrayType attribute) num_probes (methylprep.ArrayType attribute) (methylprep.models.ArrayType attribute)

num_snps (methylprep.ArrayType attribute)

P

parse_sample_sheet_into_idat_datasets() (in module methylprep) (in module methylprep.models) pipeline_find_betas_any_source() (in module methylprep.download) preprocess_noob() (in module methylprep.processing)

ProbeType (class in methylprep.models) process_all() (methylprep.processing.SampleDataContainer method) process_beta_value() (methylprep.processing.SampleDataContainer method) process_copy_number() (methylprep.processing.SampleDataContainer method) process_m_value() (methylprep.processing.SampleDataContainer method)

R

RawMetaDataset (class in methylprep.models) read() (methylprep.files.IdatDataset method) read_control_probes() (methylprep.files.Manifest method) (methylprep.Manifest method) read_mouse_probes() (methylprep.files.Manifest method) (methylprep.Manifest method) read_probes() (methylprep.Manifest method)

read_snp_probes() (methylprep.files.Manifest method) (methylprep.Manifest method) run_pipeline() (in module methylprep) (in module methylprep.processing) run_series() (in module methylprep) (in module methylprep.download) run_series_list() (in module methylprep) (in module methylprep.download)

S

Sample (class in methylprep.models) SampleDataContainer (class in methylprep.processing) SampleSheet (class in methylprep.files) search() (in module methylprep.download)

seek_to_start() (methylprep.files.Manifest static method) (methylprep.Manifest static method) set_noob() (methylprep.models.SigSet method) SigSet (class in methylprep.models) snp_data_frame (methylprep.Manifest attribute)

U

update_probe_means() (methylprep.models.SigSet method)