Index

A

Acquisition (class in pcpfm.Acquisition) add_acquisition() (pcpfm.Experiment.Experiment method) annotation_summary() (pcpfm.Report.Report method)

asari() (pcpfm.Experiment.Experiment method) (pcpfm.main.Main static method) assemble() (pcpfm.main.Main static method) assemble_study() (pcpfm.main.Main static method)

B

batch_correct() (pcpfm.FeatureTable.FeatureTable method) (pcpfm.main.Main static method) batches() (pcpfm.Experiment.Experiment method)

blank_mask() (pcpfm.FeatureTable.FeatureTable method) blank_masking() (pcpfm.main.Main static method) build_empCpds() (pcpfm.main.Main static method)

C

clean_columns() (pcpfm.FeatureTable.FeatureTable method) CLI() (in module pcpfm.main) command_history() (pcpfm.Report.Report method) computational_performance() (pcpfm.Report.Report method) construct_experiment_from_CSV() (pcpfm.Experiment.Experiment static method) construct_from_feature_table() (pcpfm.EmpCpds.EmpCpds static method)

convert() (pcpfm.main.Main static method) convert_raw_to_mzML() (pcpfm.Experiment.Experiment method) correlation_heatmap() (pcpfm.FeatureTable.FeatureTable method) create_acquisition() (pcpfm.Acquisition.Acquisition static method) create_annotation_table() (pcpfm.EmpCpds.EmpCpds method) create_experiment() (pcpfm.Experiment.Experiment static method) create_sample_annotation_table() (pcpfm.Experiment.Experiment method)

D

delete() (pcpfm.main.Main static method) delete_empCpds() (pcpfm.Experiment.Experiment method) delete_feature_table() (pcpfm.Experiment.Experiment method) download_extras() (pcpfm.main.Main static method) drop_invariants() (pcpfm.FeatureTable.FeatureTable method) drop_missing_features() (pcpfm.FeatureTable.FeatureTable method) (pcpfm.main.Main static method)

drop_outliers() (pcpfm.main.Main static method) drop_sample_by_name() (pcpfm.FeatureTable.FeatureTable method) drop_samples() (pcpfm.main.Main static method) drop_samples_by_field() (pcpfm.FeatureTable.FeatureTable method) drop_samples_by_filter() (pcpfm.FeatureTable.FeatureTable method) drop_samples_by_qaqc() (pcpfm.FeatureTable.FeatureTable method)

E

empcpd_summary() (pcpfm.Report.Report method) EmpCpds (class in pcpfm.EmpCpds)

Experiment (class in pcpfm.Experiment) experiment_summary() (pcpfm.Report.Report method)

F

feature_distribution() (pcpfm.FeatureTable.FeatureTable method) feature_distribution_outlier_detection() (pcpfm.FeatureTable.FeatureTable method) feature_id_to_khipu_id (pcpfm.EmpCpds.EmpCpds property) FeatureTable (class in pcpfm.FeatureTable)

figure() (pcpfm.Report.Report method) filter() (pcpfm.Acquisition.Acquisition method) filter_samples() (pcpfm.Experiment.Experiment method) finish() (pcpfm.main.Main static method) footer() (pcpfm.Report.ReportPDF method)

G

gen_figure() (pcpfm.FeatureTable.FeatureTable method) generate_cosmetic() (pcpfm.FeatureTable.FeatureTable method) generate_cosmetic_map() (pcpfm.Experiment.Experiment method) generate_figure_params() (pcpfm.FeatureTable.FeatureTable method) generate_output() (pcpfm.Experiment.Experiment method) (pcpfm.main.Main static method)

get_mz_tree() (pcpfm.EmpCpds.EmpCpds method) (pcpfm.FeatureTable.FeatureTable method) get_precursor_mz_tree() (pcpfm.EmpCpds.EmpCpds method) get_precursor_rt_tree() (pcpfm.EmpCpds.EmpCpds method) get_rt_tree() (pcpfm.EmpCpds.EmpCpds method) (pcpfm.FeatureTable.FeatureTable method)

H

has_ms2 (pcpfm.Acquisition.Acquisition property)

header() (pcpfm.Report.ReportPDF method)

I

impute() (pcpfm.main.Main static method) impute_missing_features() (pcpfm.FeatureTable.FeatureTable method) intensity_analysis() (pcpfm.FeatureTable.FeatureTable method)

intensity_distribution() (pcpfm.FeatureTable.FeatureTable method) ionization_mode (pcpfm.Acquisition.Acquisition property) (pcpfm.Experiment.Experiment property)

J

json_repr (pcpfm.Acquisition.Acquisition property)

K

khipu_id_to_feature_id (pcpfm.EmpCpds.EmpCpds property)

L

l1a_annotate() (pcpfm.EmpCpds.EmpCpds method) (pcpfm.main.Main static method) l1b_annotate() (pcpfm.EmpCpds.EmpCpds method) (pcpfm.main.Main static method) l2_annotate() (pcpfm.EmpCpds.EmpCpds method) (pcpfm.main.Main static method) l4_annotate() (pcpfm.EmpCpds.EmpCpds method) (pcpfm.main.Main static method)

load() (pcpfm.EmpCpds.EmpCpds static method) (pcpfm.Experiment.Experiment static method) (pcpfm.FeatureTable.FeatureTable static method) load_acquisition() (pcpfm.Acquisition.Acquisition static method) log_transform() (pcpfm.FeatureTable.FeatureTable method) (pcpfm.main.Main static method) log_transformed (pcpfm.FeatureTable.FeatureTable property)

M

Main (class in pcpfm.main) main() (in module pcpfm.main) make_nonnegative() (pcpfm.FeatureTable.FeatureTable method) map_ms2() (pcpfm.EmpCpds.EmpCpds method) (pcpfm.main.Main static method) median_correlation_outlier_detection() (pcpfm.FeatureTable.FeatureTable method) missing_feature_distribution() (pcpfm.FeatureTable.FeatureTable method) missing_feature_percentiles() (pcpfm.FeatureTable.FeatureTable method) MissingFeatureZScores() (pcpfm.FeatureTable.FeatureTable method)

module pcpfm.Acquisition pcpfm.EmpCpds pcpfm.Experiment pcpfm.FeatureTable pcpfm.main pcpfm.Report ms2_acquisitions (pcpfm.Experiment.Experiment property) ms2_spectra (pcpfm.EmpCpds.EmpCpds property)

N

non_sample_columns (pcpfm.FeatureTable.FeatureTable property) normalize() (pcpfm.main.Main static method) num_features (pcpfm.EmpCpds.EmpCpds property) (pcpfm.FeatureTable.FeatureTable property)

num_khipus (pcpfm.EmpCpds.EmpCpds property) num_samples (pcpfm.FeatureTable.FeatureTable property)

O

order_samples() (pcpfm.Experiment.Experiment method)

P

pca() (pcpfm.FeatureTable.FeatureTable method) pcpfm.Acquisition module pcpfm.EmpCpds module pcpfm.Experiment module pcpfm.FeatureTable module

pcpfm.main module pcpfm.Report module preprocess() (pcpfm.main.Main static method) process_params() (pcpfm.main.Main static method) properties_distribution() (pcpfm.FeatureTable.FeatureTable method)

Q

QAQC() (pcpfm.FeatureTable.FeatureTable method) (pcpfm.main.Main static method)

qaqc_result_to_key (pcpfm.FeatureTable.FeatureTable attribute)

R

Report (class in pcpfm.Report) report() (pcpfm.main.Main static method)

ReportPDF (class in pcpfm.Report) retrieve_empCpds() (pcpfm.Experiment.Experiment method) retrieve_feature_table() (pcpfm.Experiment.Experiment method)

S

sample_columns (pcpfm.FeatureTable.FeatureTable property) sample_names (pcpfm.Experiment.Experiment property) save() (pcpfm.EmpCpds.EmpCpds method) (pcpfm.Experiment.Experiment method) (pcpfm.FeatureTable.FeatureTable method) (pcpfm.Report.Report method)

save_fig_path() (pcpfm.FeatureTable.FeatureTable method) search_for_feature() (pcpfm.EmpCpds.EmpCpds method) (pcpfm.FeatureTable.FeatureTable method) subdirectories (pcpfm.Experiment.Experiment attribute) summarize() (pcpfm.Experiment.Experiment method) (pcpfm.main.Main static method)

T

table_summary() (pcpfm.Report.Report method) TIC() (pcpfm.Acquisition.Acquisition method) TIC_normalize() (pcpfm.FeatureTable.FeatureTable method)

TICs() (pcpfm.Report.Report method) timestamp() (pcpfm.Report.Report method) tsne() (pcpfm.FeatureTable.FeatureTable method)

U

update_annotations() (pcpfm.EmpCpds.EmpCpds method)

V

version_summary() (pcpfm.Report.Report method)