Package index • molpathR

Parsers

Functions for reading molecular pathology data files

mp_read_vcf(): Read a VCF file
mp_read_fastq(): Read a FASTQ file
mp_read_bam(): Read a BAM file
mp_read_xml_report(): Read an XML variant report
mp_read_pdf_report(): Read a PDF pathology report
mp_read_nexus_pathology(): Read Nexus pathology data
mp_read_nexus_clinical(): Read Nexus clinical data
mp_read_survival(): Read survival / outcome data
mp_read_auto(): Automatically read a molecular pathology file

Database

Build and manage the in-memory database

mp_build_db(): Build a molpath_db from parsed data objects
mp_add_data(): Add parsed data to an existing molpath_db
mp_merge_db(): Merge two molpath_db objects
mp_validate_db(): Validate a molpath_db for referential integrity and completeness
mp_save_db(): Save a molpath_db to disk
mp_load_db(): Load a molpath_db from disk

Queries

Filter and search the database

mp_query_patients(): Filter patients in a molpath_db
mp_query_variants(): Filter variants in a molpath_db
mp_query_samples(): Filter samples in a molpath_db
mp_get_patient(): Get all data for a single patient
mp_summary(): Cohort-level summary of a molpath_db
mp_search(): Free-text search across a molpath_db

Visualization

Publication-ready plots

mp_plot_variant_landscape(): Plot variant landscape (oncoplot)
mp_plot_mutation_spectrum(): Plot mutation spectrum
mp_plot_survival(): Plot Kaplan-Meier survival curves
mp_plot_cohort_overview(): Plot cohort overview
mp_plot_vaf_distribution(): Plot variant allele frequency distribution
mp_plot_timeline(): Plot patient timeline

Shiny

Interactive application

mp_run_app(): Launch the molpathR Shiny application

Data

Example data generation

mp_example_db(): Create a synthetic molecular pathology database
mp_example_files(): Write synthetic example files to a directory

Classes

S3 class constructors

new_molpath_db(): Create a new molpath_db object
new_molpath_parsed(): Create a new molpath_parsed object
validate_molpath_db(): Validate a molpath_db object
print(<molpath_db>): Print a molpath_db object
print(<molpath_parsed>): Print a molpath_parsed object
summary(<molpath_db>): Summarise a molpath_db object
summary(<molpath_parsed>): Summarise a molpath_parsed object