omicsTools1.1.7 package

Calculate Cook's Distance

Calculate Local Outlier Factor (LOF)

Calculate Measures for Each Feature

Calculate QC Statistics and RSD

Check and Sort Columns, Compare Values

Check Match

Combine Multiple Logical Tibbles with Intersection or Union

Convert MRM Data to Wide Format

Convert to Binary Matrix for UpSetR

Constructor for OmicsData

Define Anomaly Thresholds

Detect Duplicate MRM Transitions

Ensure There Are Enough Sets for UpSet Plot

Flag Anomalies

Flag Underexpressed Features in Samples Based on Blank Samples

Generate High-Dimensional Data with Anomalies

Generate Process Report for Sciex 7500/5500 Raw Data

Handle Missing Values in a Tibble

Initialize Results Data Frame

Internal Standard Normalize

Load and Parse SCIEX OS Exported LC-MRM-MS2 Data

MS1 Annotation

OmicsData Class

Perform Principal Variance Component Analysis for Batch Effect Assessm...

Perform Feature Selection

Plot PVCA results (pie chart)

Pipe operator

Plot Distribution Measures

Plot and Analyze Lipid Class Data

Plot and Analyze Metabolomics Data Summary

Plot Sample Measures

Perform Probabilistic Quotient Normalization for intensities

Prepare Data for UpSet Plot

Process All MRM Transitions for Duplicates

Plot PVCA results (bar chart)

QC-RLSC Normalize function

Run the Shiny Application

Transpose DataFrame