Omics Data Process Toolbox

---

Documentation for package ‘omicsTools’ version 1.1.7

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

Help Pages

calculate_cooks_distance	Calculate Cook's Distance
calculate_lof	Calculate Local Outlier Factor (LOF)
calculate_measures	Calculate Measures for Each Feature
calculate_measures-method	Calculate Measures for Each Feature
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
convert_mrm_data	Convert MRM Data to Wide Format
convert_to_binary_matrix	Convert to Binary Matrix for UpSetR
convert_to_binary_matrix-method	Convert to Binary Matrix for UpSetR
createOmicsData	Constructor for OmicsData
define_thresholds	Define Anomaly Thresholds
detect_duplicates	Detect Duplicate MRM Transitions
ensure_enough_sets_for_upset	Ensure There Are Enough Sets for UpSet Plot
ensure_enough_sets_for_upset-method	Ensure There Are Enough Sets for UpSet Plot
flag_anomalies	Flag Anomalies
flag_anomalies-method	Flag Anomalies
flag_underexpressed_features	Flag Underexpressed Features in Samples Based on Blank Samples
generate_data_with_anomalies	Generate High-Dimensional Data with Anomalies
generate_process_report	Generate Process Report for Sciex 7500/5500 Raw Data
handle_missing_values	Handle Missing Values in a Tibble
initialize_results_df	Initialize Results Data Frame
internal_standard_normalize	Internal Standard Normalize
load_parse_sciex_txt	Load and Parse SCIEX OS Exported LC-MRM-MS2 Data
ms1_annotation	MS1 Annotation
OmicsData-class	OmicsData Class
perform_batch_assessment	Perform Principal Variance Component Analysis for Batch Effect Assessment
perform_feature_selection	Perform Feature Selection
pieDraw	Plot PVCA results (pie chart)
plot_distribution_measures	Plot Distribution Measures
plot_distribution_measures-method	Plot Distribution Measures
plot_lipid_data_summary	Plot and Analyze Lipid Class Data
plot_met_data_summary	Plot and Analyze Metabolomics Data Summary
plot_sample_measures	Plot Sample Measures
plot_sample_measures-method	Plot Sample Measures
pqn_normalize	Perform Probabilistic Quotient Normalization for intensities
prepare_upset_data	Prepare Data for UpSet Plot
prepare_upset_data-method	Prepare Data for UpSet Plot
process_mrm_duplicates	Process All MRM Transitions for Duplicates
pvcaDraw	Plot PVCA results (bar chart)
qc_normalize	QC-RLSC Normalize function
run_app	Run the Shiny Application
transpose_df	Transpose DataFrame