Package index • mums2

Import Data

import_all_data(): Import all data

Add Ms2 Data

ms2_ms1_compare(): Match your ms1 spectra to a ms2

Reference Database Readers

read_msp(): Create Reference Database
read_hmdb(): Read HMDB database
combined_reference_database(): Combine Databases
get_reference_data(): Get Reference Data
length(<reference_database>): Reference database length
print(<reference_database>): Print reference

Filters

filter_peak_table(): Filter Peak Table
filter_mispicked_ions_params(): Filter Mispicked Ions Parameters
filter_group_params(): Filter Group Parameters
filter_cv_params(): Filter Cv Parameters
filter_insource_ions_params(): Filter Insource Ions Parameters

Annotation

annotate_ms2(): Annotate LC-MS/MS features

Scoring

dist_ms2(): Calculate pairwise distance between MS/MS features.
modified_cosine_params(): GNPS-like similarity between two MS/MS spectra
spec_entropy_params(): Entropy similarity between two MS/MS spectra

Cluster

cluster_data(): Cluster Features

Diversity Metrics

rarefy_ms(): Rarefy MS1 Feature Table
dist_shared(): Distance Shared
alpha_summary(): Alpha Diversity Summary

Community Object

create_community_matrix(): create community matrix
create_community_matrix_object(): Create Community Matrix Object.
print(<community_object>): Print Community Object
get_community_matrix(): Get Community Matrix

Example Data

mums2_example(): Get file paths for examples

De-novo Molecular Formula Predictions

compute_molecular_formulas(): Compute Molecular formula

Helper Functions

change_rt_to_seconds_or_minute(): Change RT time to minutes or seconds
generate_a_combined_table(): Create a combined table
convert_to_group_averages(): Convert Samples to Group Averages