Package index • pmotoolsr

Package overview

pmotoolsr pmotoolsr-package: pmotoolsr: Toolkit for working with Portable Microhaplotype Objects (PMOs)

Reading & writing PMOs

Read and write Portable Microhaplotype Object files (plain or gzip / bzip2 / xz compressed), as R6 objects or as raw nested lists.

read_pmo(): Read a PMO object from a file
write_pmo(): Write a PMO object to a file
read_pmo_raw(): Read a PMO file as a raw nested list
write_pmo_raw(): Write a raw PMO nested list to a file
pmo_list_to_r6(): Convert a raw PMO list into a PortableMicrohaplotypeObject

Validation & schema

Validate a PMO against the JSON Schema and inspect schema versions and field requirements.

pmo_validate(): Validate a PMO (structural and, by default, schema)
pmo_validate_jsonschema(): Validate a PMO against the JSON Schema
pmo_check_required_base_fields(): Check that a PMO has all required top-level fields
pmo_required_fields_for_class(): Get the required fields for a PMO schema class
pmo_load_schema(): Load a bundled PMO JSON schema
pmo_load_schema_by_version(): Load a bundled PMO JSON schema by version
pmo_schema_version(): Default PMO schema version targeted by this package
pmo_has_section(): Test whether an optional PMO section is present and non-empty

Processing & querying

Look up names and indices, count entities, and subset / filter a PMO down to selected specimens, library samples, targets, metadata groups, or read depth.

pmo_get_specimen_names() pmo_get_sorted_specimen_names() pmo_get_library_sample_names() pmo_get_sorted_library_sample_names() pmo_get_target_names() pmo_get_sorted_target_names() pmo_get_panel_names() pmo_get_sorted_panel_names() pmo_get_bioinformatics_run_names() pmo_get_sorted_bioinformatics_run_names(): Get entity names from a PMO
pmo_index_key_specimen_names() pmo_index_key_library_sample_names() pmo_index_key_target_names() pmo_index_key_panel_names() pmo_index_key_bioinformatics_run_names(): Build a name-to-index lookup for PMO entities
pmo_index_key_target_in_representative_microhaplotypes(): Build a target-name to representative-microhaplotype-index lookup
pmo_index_of_specimen_names() pmo_index_of_library_sample_names() pmo_index_of_target_names() pmo_index_of_panel_names() pmo_index_of_bioinformatics_run_names() pmo_index_of_target_in_representative_microhaplotypes(): Resolve entity names to their 1-based PMO indices
pmo_library_ids_for_specimen_ids(): Get library sample ids for a set of specimen ids
pmo_count_library_samples_per_target(): Count the number of library samples a target is detected in
pmo_count_specimen_by_field_value(): Count specimens grouped by combinations of metadata field values
pmo_count_specimen_per_meta_fields(): Count how many specimens carry each metadata field
pmo_count_targets_per_library_sample(): Count the number of targets detected per library sample
pmo_count_targets_per_panel(): Count the number of unique targets in each panel
pmo_filter_by_library_sample_ids(): Filter a PMO down to selected library samples
pmo_filter_by_library_sample_names(): Filter a PMO down to selected library samples by name
pmo_filter_by_specimen_ids(): Filter a PMO down to selected specimens
pmo_filter_by_specimen_names(): Filter a PMO down to selected specimens by name
pmo_filter_by_target_ids(): Filter a PMO down to selected targets
pmo_filter_by_target_names(): Filter a PMO down to selected targets by name
pmo_extract_by_read_filter(): Filter detected microhaplotypes by a minimum read count
pmo_extract_samples_by_meta_groupings(): Extract specimens matching metadata groupings
pmo_extract_allele_counts_freq(): Extract allele (microhaplotype) counts and frequencies

Exporting tables

Flatten PMO sections into tibbles and export allele tables, BED files, and Excel workbooks.

pmo_export_bioinformatics_methods_info_meta_table(): Export bioinformatics methods info metadata
pmo_export_bioinformatics_run_info_meta_table(): Export bioinformatics run info metadata
pmo_export_library_sample_meta_table(): Export library sample metadata
pmo_export_panel_info_meta_table(): Export panel info metadata
pmo_export_pmo_header_table(): Export PMO header metadata
pmo_export_project_info_meta_table(): Export project info metadata
pmo_export_sequencing_info_meta_table(): Export sequencing info metadata
pmo_export_specimen_meta_table(): Export specimen metadata
pmo_export_specimen_travel_meta_table(): Export specimen travel metadata
pmo_export_target_info_meta_table(): Export target info metadata
pmo_export_targeted_genomes_meta_table(): Export targeted genomes metadata
pmo_export_to_excel(): Export a PMO to a multi-sheet Excel workbook
pmo_extract_alleles_per_sample_table(): Extract a per-sample allele table
pmo_list_library_samples_per_specimen(): List library sample names per specimen
pmo_extract_targets_insert_bed(): Extract target insert locations as BED rows
pmo_extract_panels_insert_bed(): Extract panel insert locations as BED rows
pmo_write_bed(): Write BED rows to a file

Building & combining PMOs

Assemble PMOs from tabular inputs, merge components into a single object, update metadata, and combine multiple PMOs.

pmo_library_sample_info_table_to_pmo(): Convert a library-sample metadata table into PMO library_sample_info
pmo_mhap_table_to_pmo(): Convert a microhaplotype calls table into PMO microhaplotype structures
pmo_panel_info_table_to_pmo(): Convert a panel/target table into PMO target_info + panel_info
pmo_read_count_by_stage_table_to_pmo(): Convert read-count tables into the PMO read_counts_by_stage structure
pmo_specimen_info_table_to_pmo(): Convert a specimen metadata table into PMO specimen_info
pmo_minimum_library_specimen_from_mhap_table(): Build minimal library/specimen info from a detected-microhaplotypes structure
pmo_merge_panel_info_dicts(): Merge multiple panel_info dictionaries
pmo_merge_to_pmo(): Merge name-based PMO components into a complete PMO
pmo_combine_pmos(): Combine multiple PMOs into a single PMO
pmo_update_specimen_with_traveler_info(): Add travel history to a PMO's specimens
pmo_merge_dicts_by_key(): Merge two lists of dicts by a shared key field

PMO classes

Auto-generated R6 classes mirroring the PMO schema. Most users interact with these through read_pmo() / write_pmo() rather than constructing them directly.

PortableMicrohaplotypeObject: PortableMicrohaplotypeObject
BioMethod: BioMethod
BioinformaticsMethodInfo: BioinformaticsMethodInfo
BioinformaticsRunInfo: BioinformaticsRunInfo
DetectedMicrohaplotypes: DetectedMicrohaplotypes
DetectedMicrohaplotypesForSample: DetectedMicrohaplotypesForSample
DetectedMicrohaplotypesForTarget: DetectedMicrohaplotypesForTarget
GenomeInfo: GenomeInfo
GenomicLocation: GenomicLocation
LibrarySampleInfo: LibrarySampleInfo
MarkerOfInterest: MarkerOfInterest
MaskingInfo: MaskingInfo
MicrohaplotypeForTarget: MicrohaplotypeForTarget
PanelInfo: PanelInfo
ParasiteDensity: ParasiteDensity
PlateInfo: PlateInfo
PmoGenerationMethod: PmoGenerationMethod
PmoHeader: PmoHeader
PrimerInfo: PrimerInfo
ProjectInfo: ProjectInfo
ProteinVariant: ProteinVariant
Pseudocigar: Pseudocigar
ReactionInfo: ReactionInfo
ReadCountsByStage: ReadCountsByStage
ReadCountsByStageForLibrarySample: ReadCountsByStageForLibrarySample
ReadCountsByStageForTarget: ReadCountsByStageForTarget
RepresentativeMicrohaplotype: RepresentativeMicrohaplotype
RepresentativeMicrohaplotypes: RepresentativeMicrohaplotypes
RepresentativeMicrohaplotypesForTarget: RepresentativeMicrohaplotypesForTarget
SequencingInfo: SequencingInfo
SpecimenInfo: SpecimenInfo
StageReadCounts: StageReadCounts
TargetInfo: TargetInfo
TravelInfo: TravelInfo