Microbial Ecology by Tandem Mass Spectrometry

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Documentation for package ‘mums2’ version 0.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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