Omics Data Processing Toolbox

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Documentation for package ‘omicsTools’ version 2.0.0

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

Help Pages

calculate_qc_rsd	Calculate QC Statistics and RSD
check_and_sort_columns	Check and Sort Columns, Compare Values
check_match	Check Match
combine_logical_tibbles	Combine Multiple Logical Tibbles with Intersection or Union
compare_omics_groups	Compare two groups of samples
convert_mrm_data	Convert MRM Data to Wide Format
detect_duplicates	Detect Duplicate MRM Transitions
detect_sample_outliers	Detect multivariate sample outliers
export_omics_results	Export a complete workflow result
filter_blank_features	Filter features against blank samples
filter_missing_value	Filter features by missing-value rate
filter_qc_rsd	Filter features by quality-control relative standard deviation
fit_targeted_calibration	Fit a targeted-assay calibration model
flag_underexpressed_features	Flag Underexpressed Features in Samples Based on Blank Samples
generate_process_report	Generate Process Report for Sciex 7500/5500 Raw Data
generate_sample_metadata	Generate sample metadata from file or sample names
handle_missing_values	Handle Missing Values in a Tibble
impute_half_min	Impute missing values with half of a feature minimum
internal_standard_normalize	Internal Standard Normalize
load_data	Load omics data
load_omics_data	Load an omics dataset
load_parse_sciex_txt	Load and Parse SCIEX OS Exported LC-MRM-MS2 Data
ms1_annotation	Annotate MS1 mass-to-charge values
omics_example_file	Locate a bundled plot example
omics_gui_capabilities	Available omicsTools workflows
plot_lcms_features	Plot detected LC-MS features by retention time and m/z
plot_lipid_data_summary	Plot and Analyze Lipid Class Data
plot_met_data_summary	Plot and Analyze Metabolomics Data Summary
plot_omics_heatmap	Plot a feature intensity heatmap
plot_omics_pca	Compute and plot principal components for omics data
plot_peak_list	Plot a tandem mass spectrum
plot_targeted_calibration	Plot a targeted calibration curve
pqn_normalize	Perform Probabilistic Quotient Normalization for intensities
predict_targeted_calibration	Predict concentrations with a targeted calibration model
process_mrm_duplicates	Process All MRM Transitions for Duplicates
process_omics_data	Process an omics feature table
qc_normalize	QC-RLSC Normalize function
run_app	Run the omicsTools application
save_msp	Write a spectrum in MSP format
transpose_df	Transpose a feature table using its first column as identifiers
validate_omics_data	Validate and align omics tables
write_omics_report	Write a self-contained workflow QC report