Function reference • clamr

Core Data Structures Represent datasets and properties
Working with .mzrollDB experiments Connect to an mzrollDB sqlite database produced by MAVEN or quahog.
`clamr`	`clamr` package
`mzroll_db_sqlite()`	mzrollDB file (SQLite)
`clamr_summary()`	CLaM R Summary
`test_mzroll_db_con_schema()`	Test mzrollDB Connection Schema
`validate_mzroll_db_schema()`	Validate mzrollDB Schema
`mzroll_pass_bookmarks()`	Mzroll Pass Bookmarks
CLaM R Config Specify parameters tied to a mass spec experiment such as mass tolerances.
`build_clamr_config()`	Build CLaM R config
`clamr_config_assign()`	CLaM R Config Assign
`format_mass_accuracy_input()`	Format Mass Accuracy Input
`format_mass_accuracy_tolerances()`	Format mass accuracy tolerances
`require_tolerances()`	CLaM R require tolerances
`test_clamr_config()`	Test CLaM R config
Alternative Data Representations
`extract_peakset()`	Extract Peakset
`peakset_format_for_mzroll()`	Peakset Format for Mzroll
`augment_peakgroups()`	Augment Peak Groups
`nest_peakgroup_features()`	Nest Peak Groups
`mz_set_example`	Example data set with peak group precursor m/z, RT, and MS2 scan information.
Raw data workflows Interact with mass spec files rather than an .mzrollDB dataset
`tidy_mzR_from_msfile()`	Read a mass spec file with mzR
`tidy_mzR_extract_mzs()`	Extract Masses with mzR
`tidy_mzR_EICs()`	Generated Extracted Ion Chromatographs using mzR
`tidy_mzR_plot_scans()`	Plot mzR scans
`tidy_mzR_plot_major_features()`	Find Major Features
`match_mzroll_db_to_file()`	Match .mzrollDB to file
`strip_ms_file_extension()`	Strip file extension
`strip_ms_file_extension_from_extensions()`	package-local function that does the actual work of modifying file extensions.
`get_valid_ms_file_extensions()`	Get all valid file extensions
`ms2_scans_from_raw_files()`	MS2 Scans from files
Dataset-Level Transformation and Identification Update an experiment
Retention Time Alignment Align samples to correct for RT drift
`ms2_driven_aligner()`	MS2 Driven Aligner
`estimate_rt_drift()`	Estimate RT Drift
`estimate_mz_ppm_drift()`	Estimate M/Z ppm Drift
`ms2_driven_aligner_plotting()`	MS2 Driven Aligner Plotting
`find_candidate_anchors()`	Find Candidate Anchor Points
`update_sample_rt()`	Update Sample Retention Time
Coelution Detection Detect features which are related isotopologues or adducts
`identify_coelutions()`	Identify Coelutions
`find_common_coelutions()`	Find Common Coelutions
`simplify_coelution_subgraph()`	Simplify Coelution Clique
`apply_coelution_labels()`	Apply Coelution Labels
`generate_coelution_peaks()`	Generate Coelution Peaks
`combine_sample_coelutions_w_peaks()`	Combine Sample Coelutions with Peaks
`peakgrp_coelution_annotation()`	Label Coelutions
`standard_coelution_library`	Table of standard coelutions, including m/z difference and atomic description.
Detect Pathologies Identify complex noise
`identify_split_peaks()`	Identify Split Peaks
`smear_detection()`	Smear Detection
Dataset Filters Remove peakgroups or samples from a .mzrollDB experiment file
`find_unique_peakgroups()`	Find Unique Peakgroups
`merge_peakgroups()`	Merge Peakgroups
`remove_redundant_peakgroups()`	Remove Redundant Peakgroups
`reduce_mzroll_samples()`	Reduce mzroll samples
Spectra Group, filter, and match spectra
`extract_fragments()`	Extract fragments only
Grouping
`find_consistent_ms2_fingerprints()`	Find Consistent MS2 Fingerprints
`group_similar_MS2()`	Group Similar MS2
`score_fragmentation_similarity()`	Score Fragmentation Similarity
`extract_and_group_fragments()`	Extract and group fragments
`aggregate_scans()`	Aggregate Scans
`sum_spectra()`	Sum Spectra
Filtering
`spectra_filter_fragments()`	Spectra Filter Fragments
`filter_low_complexity_spectra()`	Filter Low Complexity Spectra
`filter_low_information_fragments()`	Filter Low Information Fragments
Utilities
Clustering Separate features into resolvable subsets
`find_mz_jumps()`	Find M/Z Jumps
`find_scan_jumps()`	Returns a vector of grouped scans -- each group is defined by a separation of less than tolerances
`find_density_minima()`	Separate by local minima
Joins Join features by mass and retention time
`join_peaks_to_scans()`	Join peaks to scans when their is a scan range and mz match for a given sample
`join_groupIds_to_mz_rts()`	Join GroupIds to mz/z, rt
`join_matching_standards()`	Join Matching Standards
`match_peaksets()`	Match Peaksets
`mz_peak_join_fxn()`	Match peaks to peaks for a single sample
`mz_scan_join_fxn()`	Match scans to peaks for a single sample
Chemistry Work with chemical formulas
`parse_standard_formulas()`	Parse formulas
`create_isotopic_chemical_formula()` `parse_isotopic_chemical_formula()`	Create chemical formula
`estimate_chemical_formula()`	Estimate chemical formula
`split_formula()`	Split formula
`formula_monoisotopic_mass()`	Formula Monoisotopic Mass
`adduct_mass()`	Adduct Mass
`isotope_summaries`	Table of isotope information, including m/z and frequency
`elemental_frequency_summary`	Table of isotopic information, and relative abundance in various media

Reference

Core Data Structures

Working with .mzrollDB experiments

CLaM R Config

Alternative Data Representations

Raw data workflows

Dataset-Level Transformation and Identification

Retention Time Alignment

Coelution Detection

Detect Pathologies

Dataset Filters

Spectra

Grouping

Filtering

Utilities

Clustering

Joins

Chemistry