Function reference • claman

Primary Workflow The primary building blocks of an analysis
Connecting to Data and Standards Operations for starting an analyssis
`process_mzroll()`	Process mzRoll
`process_mzroll_multi()`	Process mzroll multi
Processing and Normalization Operations which modify the working data
`normalize_peaks()` `normalize_peaks_median_polish()` `normalize_peaks_loading_value()` `normalize_peaks_batch_center()` `normalize_peaks_reference_sample()` `normalize_peaks_reference_condition()` `normalize_peaks_loess()`	Normalize Peaks
`floor_peaks()`	Floor Peaks
`collapse_injections()`	Collapse Injections
`filter_groupIds()`	Filter GroupIds
Statistics Finding metabolites/lipids with interesting patterns of variability
`diffex_mzroll()`	Differential Expression Analysis on Mzroll List
Plotting
`plot_barplot()`	Plot Barplots
`plot_compare_injection()`	Compare Injections
`plot_pvalues()`	P-value Histogram
`plot_volcano()`	Volcano plot
Export
Advanced Methods These methods are compatible with the standard workflow but have syntax which is too tricky for many users
Dev Tools Functions used behind the scenes
Sample Sheets
Data Structures
`aggregate_mzroll_nest()`	Aggregate mzroll lists
`test_mzroll_list()`	Test MzRoll List
Utils
`aggregate_mzroll_nest()`	Aggregate mzroll lists
`calculate_pathway_enrichment_fisher()`	Calculate Pathway Enrichments with a Fisher-Exact tests
`calculate_pathway_enrichment_gsea()`	Calculate Pathway Enrichments using GSEA
`calicomics`	`claman` package
`collapse_injections()`	Collapse Injections
`collapse_metabolites()`	Collapse Metabolites
`create_sqlite_con()`	Create SQLite Connection
`diffex_mzroll()`	Differential Expression Analysis on Mzroll List
`filter_groupIds()`	Filter GroupIds
`find_pathway_enrichments()`	Find Pathway Enrichments
`floor_peaks()`	Floor Peaks
`lipid_components()`	Generate relevant lipid components from compound name
`merge_compounds_tbl()`	Merge Compounds Table
`merge_samples_tbl()`	Merge Samples Table
`normalize_peaks()` `normalize_peaks_median_polish()` `normalize_peaks_loading_value()` `normalize_peaks_batch_center()` `normalize_peaks_reference_sample()` `normalize_peaks_reference_condition()` `normalize_peaks_loess()`	Normalize Peaks
`nplug_compounds`	NPLUG samples
`nplug_mzroll()`	Growth-Limiting Metabolites
`nplug_mzroll_augmented`	NPLUG MzRoll Augmented
`nplug_mzroll_normalized`	NPLUG MzRoll Normalized
`nplug_samples`	NPLUG samples
`plot_barplot()`	Plot Barplots
`plot_compare_injection()`	Compare Injections
`plot_pvalues()`	P-value Histogram
`plot_volcano()`	Volcano plot
`process_mzroll()`	Process mzRoll
`process_mzroll_identify_peakgroups()`	Process MzRoll - Identify Peakgroups
`process_mzroll_load_peakgroups()`	Process MzRoll - Load Peakgroups
`process_mzroll_multi()`	Process mzroll multi
`process_mzroll_validate_peakgroups()`	Process MzRoll - Validate Peakgroups
`remove_constant_name()`	Remove Constant Name
`test_mzroll_list()`	Test MzRoll List
`util_pretty_khead()`	Util - Pretty Knitr Head

Reference

Primary Workflow

Connecting to Data and Standards

Processing and Normalization

Statistics

Plotting

Export

Advanced Methods

Dev Tools

Sample Sheets

Data Structures

Utils