# Microbial Ecology by Tandem Mass Spectrometry

## Documentation for package ‘mums2’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

alpha_summary | Alpha Diversity Summary
annotate_ms2 | Annotate LC-MS/MS features
change_rt_to_seconds_or_minute | Change RT time to minutes or seconds
cluster_data | Cluster Features
combined_reference_database | Combine Databases
compute_molecular_formulas | Compute Molecular formula Other
convert_to_group_averages | Convert Samples to Group Averages
create_community_matrix | create community matrix
create_community_matrix_object | Create Community Matrix Object.
create_community_matrix_object.mass_data | Create Community Matrix Object.
create_community_matrix_object.mothur_cluster | Create Community Matrix Object.
dist_ms2 | Calculate pairwise distance between MS/MS features.
dist_shared | Distance Shared
filter_cv_params | Filter Cv Parameters
filter_group_params | Filter Group Parameters
filter_insource_ions_params | Filter Insource Ions Parameters
filter_mispicked_ions_params | Filter Mispicked Ions Parameters
filter_peak_table | Filter Peak Table
filter_peak_table.filter_cv | Filter Peak Table
filter_peak_table.filter_group | Filter Peak Table
filter_peak_table.filter_insource_ions | Filter Peak Table
filter_peak_table.filter_mispicked_ions | Filter Peak Table
generate_a_combined_table | Create a combined table
get_community_matrix | Get Community Matrix
get_molecular_formula_preds | Get Molecular Formula Predictions
get_ms1_data | Get MS1 Matches
get_ms2_matches | Get MS2 Matches
get_ms2_peaks_data | Get Peaks Data
get_reference_data | Get Reference Data
get_samples | Get Samples
import_all_data | Import all data
length.reference_database | Reference database length
modified_cosine_params | GNPS-like similarity between two MS/MS spectra
ms2_ms1_compare | Match your ms1 spectra to a ms2
mums2_example | Get file paths for examples
print.community_object | Print Community Object
print.reference_database | Print reference
rarefy_ms | Rarefy MS1 Feature Table
read_hmdb | Read HMDB database
read_msp | Create Reference Database
spec_entropy_params | Entropy similarity between two MS/MS spectra