Index

A

add_attribute() (dimspy.models.peaklist.PeakList method) add_flag() (dimspy.models.peak_matrix.PeakMatrix method) add_tag() (dimspy.models.peaklist_tags.PeakList_Tags method) align_peaks() (in module dimspy.process.peak_alignment) align_samples() (in module dimspy.tools)

attr_matrix() (dimspy.models.peak_matrix.PeakMatrix method) attr_mean_vector() (dimspy.models.peak_matrix.PeakMatrix method) attributes() (dimspy.models.peak_matrix.PeakMatrix property) (dimspy.models.peaklist.PeakList property) average_replicate_peaklists() (in module dimspy.process.replicate_processing) average_replicate_scans() (in module dimspy.process.replicate_processing)

B

blank_filter() (in module dimspy.tools)

C

calculate_flags() (dimspy.models.peaklist.PeakList method) cleanup_unflagged_peaks() (dimspy.models.peaklist.PeakList method) close() (dimspy.portals.mzml_portal.Mzml method) (dimspy.portals.thermo_raw_portal.ThermoRaw method)

copy() (dimspy.models.peaklist.PeakList method) count_ms_types() (in module dimspy.metadata) count_scan_types() (in module dimspy.metadata) create_sample_list() (in module dimspy.tools)

D

dimspy.metadata module dimspy.models.peak_matrix module dimspy.models.peaklist module dimspy.models.peaklist_metadata module dimspy.models.peaklist_tags module dimspy.portals.hdf5_portal module dimspy.portals.mzml_portal module dimspy.portals.paths module dimspy.portals.thermo_raw_portal module

dimspy.portals.txt_portal module dimspy.process.peak_alignment module dimspy.process.peak_filters module dimspy.process.replicate_processing module dimspy.tools module drop_all_tags() (dimspy.models.peaklist_tags.PeakList_Tags method) drop_attribute() (dimspy.models.peaklist.PeakList method) drop_flag() (dimspy.models.peak_matrix.PeakMatrix method) drop_tag() (dimspy.models.peaklist_tags.PeakList_Tags method) drop_tag_type() (dimspy.models.peaklist_tags.PeakList_Tags method) dtable() (dimspy.models.peaklist.PeakList property)

E

extract_peaklist() (dimspy.models.peak_matrix.PeakMatrix method)

extract_peaklists() (dimspy.models.peak_matrix.PeakMatrix method)

F

filter_attr() (in module dimspy.process.peak_filters) filter_blank_peaks() (in module dimspy.process.peak_filters) filter_fraction() (in module dimspy.process.peak_filters) filter_mz_ranges() (in module dimspy.process.peak_filters) filter_ringing() (in module dimspy.process.peak_filters) filter_rsd() (in module dimspy.process.peak_filters) flag_attributes() (dimspy.models.peaklist.PeakList property)

flag_names() (dimspy.models.peak_matrix.PeakMatrix property) flag_values() (dimspy.models.peak_matrix.PeakMatrix method) flags() (dimspy.models.peak_matrix.PeakMatrix property) (dimspy.models.peaklist.PeakList property) fraction() (dimspy.models.peak_matrix.PeakMatrix property) full_shape() (dimspy.models.peak_matrix.PeakMatrix property) (dimspy.models.peaklist.PeakList property) full_size() (dimspy.models.peaklist.PeakList property)

G

get_attribute() (dimspy.models.peaklist.PeakList method)

get_peak() (dimspy.models.peaklist.PeakList method)

H

has_attribute() (dimspy.models.peaklist.PeakList method) has_tag() (dimspy.models.peaklist_tags.PeakList_Tags method) has_tag_type() (dimspy.models.peaklist_tags.PeakList_Tags method)

hdf5_peak_matrix_to_txt() (in module dimspy.tools) hdf5_peaklists_to_txt() (in module dimspy.tools) headers() (dimspy.portals.mzml_portal.Mzml method) (dimspy.portals.thermo_raw_portal.ThermoRaw method)

I

ID() (dimspy.models.peaklist.PeakList property) idxs_reps_from_filelist() (in module dimspy.metadata) insert_peak() (dimspy.models.peaklist.PeakList method) intensity_matrix() (dimspy.models.peak_matrix.PeakMatrix property)

intensity_mean_vector() (dimspy.models.peak_matrix.PeakMatrix property) interpret_method() (in module dimspy.metadata) ion_injection_times() (dimspy.portals.mzml_portal.Mzml method) (dimspy.portals.thermo_raw_portal.ThermoRaw method) is_empty() (dimspy.models.peak_matrix.PeakMatrix method)

J

join_peaklists() (in module dimspy.process.replicate_processing)

L

load_peak_matrix_from_hdf5() (in module dimspy.portals.hdf5_portal) load_peak_matrix_from_txt() (in module dimspy.portals.txt_portal)

load_peaklist_from_txt() (in module dimspy.portals.txt_portal) load_peaklists() (in module dimspy.tools) load_peaklists_from_hdf5() (in module dimspy.portals.hdf5_portal)

M

mask() (dimspy.models.peak_matrix.PeakMatrix property) mask_all_peakmatrix (class in dimspy.models.peak_matrix) mask_peakmatrix (class in dimspy.models.peak_matrix) mask_tags() (dimspy.models.peak_matrix.PeakMatrix method) merge_peaklists() (in module dimspy.tools) metadata() (dimspy.models.peaklist.PeakList property) missing_values() (dimspy.models.peak_matrix.PeakMatrix property) missing_values_sample_filter() (in module dimspy.tools) mode_type_from_header() (in module dimspy.metadata) module dimspy.metadata dimspy.models.peak_matrix dimspy.models.peaklist dimspy.models.peaklist_metadata dimspy.models.peaklist_tags dimspy.portals.hdf5_portal dimspy.portals.mzml_portal dimspy.portals.paths dimspy.portals.thermo_raw_portal dimspy.portals.txt_portal dimspy.process.peak_alignment dimspy.process.peak_filters dimspy.process.replicate_processing dimspy.tools

ms_type_from_header() (in module dimspy.metadata) mz_matrix() (dimspy.models.peak_matrix.PeakMatrix property) mz_mean_vector() (dimspy.models.peak_matrix.PeakMatrix property) mz_range_from_header() (in module dimspy.metadata) (in module dimspy.portals.thermo_raw_portal) Mzml (class in dimspy.portals.mzml_portal)

O

occurrence() (dimspy.models.peak_matrix.PeakMatrix property)

P

partition() (in module dimspy.tools) PeakList (class in dimspy.models.peaklist) peaklist() (dimspy.portals.mzml_portal.Mzml method) (dimspy.portals.thermo_raw_portal.ThermoRaw method) peaklist_ids() (dimspy.models.peak_matrix.PeakMatrix property) PeakList_Metadata (class in dimspy.models.peaklist_metadata) peaklist_tag_types() (dimspy.models.peak_matrix.PeakMatrix property) peaklist_tag_values() (dimspy.models.peak_matrix.PeakMatrix property) PeakList_Tags (class in dimspy.models.peaklist_tags)

peaklist_tags() (dimspy.models.peak_matrix.PeakMatrix property) peaklists() (dimspy.portals.mzml_portal.Mzml method) (dimspy.portals.thermo_raw_portal.ThermoRaw method) PeakMatrix (class in dimspy.models.peak_matrix) peaks() (dimspy.models.peaklist.PeakList property) present() (dimspy.models.peak_matrix.PeakMatrix property) present_matrix() (dimspy.models.peak_matrix.PeakMatrix property) process_scans() (in module dimspy.tools) property() (dimspy.models.peak_matrix.PeakMatrix method) purity() (dimspy.models.peak_matrix.PeakMatrix property)

R

read_scans() (in module dimspy.process.replicate_processing) remove_edges() (in module dimspy.process.replicate_processing) remove_empty_peaks() (dimspy.models.peak_matrix.PeakMatrix method) remove_peak() (dimspy.models.peaklist.PeakList method)

remove_peaks() (dimspy.models.peak_matrix.PeakMatrix method) remove_samples() (dimspy.models.peak_matrix.PeakMatrix method) (in module dimspy.tools) replicate_filter() (in module dimspy.tools) rsd() (dimspy.models.peak_matrix.PeakMatrix method)

S

sample_filter() (in module dimspy.tools) save_peak_matrix_as_hdf5() (in module dimspy.portals.hdf5_portal) save_peak_matrix_as_txt() (in module dimspy.portals.txt_portal) save_peaklist_as_txt() (in module dimspy.portals.txt_portal) save_peaklists_as_hdf5() (in module dimspy.portals.hdf5_portal) scan_dependents() (dimspy.portals.mzml_portal.Mzml method) (dimspy.portals.thermo_raw_portal.ThermoRaw method) scan_ids() (dimspy.portals.mzml_portal.Mzml method) (dimspy.portals.thermo_raw_portal.ThermoRaw method)

scan_type_from_header() (in module dimspy.metadata) set_attribute() (dimspy.models.peaklist.PeakList method) set_peak() (dimspy.models.peaklist.PeakList method) shape() (dimspy.models.peak_matrix.PeakMatrix property) (dimspy.models.peaklist.PeakList property) size() (dimspy.models.peaklist.PeakList property) sort_ms_files_by_timestamp() (in module dimspy.portals.paths) sort_peaks_order() (dimspy.models.peaklist.PeakList method)

T

Tag (class in dimspy.models.peaklist_tags) tag_of() (dimspy.models.peaklist_tags.PeakList_Tags method) tag_types() (dimspy.models.peaklist_tags.PeakList_Tags property) tag_values() (dimspy.models.peaklist_tags.PeakList_Tags property) tags() (dimspy.models.peaklist.PeakList property) (dimspy.models.peaklist_tags.PeakList_Tags property) tags_of() (dimspy.models.peak_matrix.PeakMatrix method) ThermoRaw (class in dimspy.portals.thermo_raw_portal) tics() (dimspy.portals.mzml_portal.Mzml method) (dimspy.portals.thermo_raw_portal.ThermoRaw method) to_df() (dimspy.models.peaklist.PeakList method)

to_dict() (dimspy.models.peaklist.PeakList method) to_int() (in module dimspy.metadata) to_list() (dimspy.models.peaklist.PeakList method) (dimspy.models.peaklist_tags.PeakList_Tags method) to_peaklist() (dimspy.models.peak_matrix.PeakMatrix method) to_str() (dimspy.models.peak_matrix.PeakMatrix method) (dimspy.models.peaklist.PeakList method) (dimspy.models.peaklist_tags.PeakList_Tags method) ttype() (dimspy.models.peaklist_tags.Tag property) typed() (dimspy.models.peaklist_tags.Tag property) typed_tags() (dimspy.models.peaklist_tags.PeakList_Tags property)

U

unmask_all_peakmatrix (class in dimspy.models.peak_matrix) unmask_peakmatrix (class in dimspy.models.peak_matrix) unmask_tags() (dimspy.models.peak_matrix.PeakMatrix method)

untyped_tags() (dimspy.models.peaklist_tags.PeakList_Tags property) update_labels() (in module dimspy.metadata) update_metadata_and_labels() (in module dimspy.metadata)

V

validate_and_sort_paths() (in module dimspy.portals.paths)

validate_metadata() (in module dimspy.metadata) value() (dimspy.models.peaklist_tags.Tag property)