R: Omics Data Process Toolbox

# Omics Data Process Toolbox

## Documentation for package ‘omicsTools’ version 1.1.7

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

## 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