Contents | 1. Introduction | 2. Installation | Prerequisites | Installing Dependencies | Installing PCA-PAM50 | Loading PCA-PAM50 and Dependencies | 3. Deriving PCAPAM50 Calls Using Provided Test Data | 3.1. Pipeline Overview | 3.1.1. makeCalls.PC1ihc - Intermediate Intrinsic Subtype Calls | 1) Load the Test data | 2) Prepare the Data | 3) Create the Clinical Subtype Data Frame | 4) Call the Function | 3.1.2. makeCalls.v1PAM - PCAPAM50 Calls | Call the Function | 3.2. The Conventional PAM50 Approach | 3.2.1. makeCalls.ihc - Conventional PAM50 Intrinsic Subtype Calls | 3.3. - Plotting Data | 3.3.1. - my.plotPCA - | 4. Comparing Results - PCAPAM50 vs PAM50 | 4.1. Test Data - PCAPAM50 vs PAM50 | 4.2. TCGA Data - PCAPAM50 vs PAM50 | 1) Load TCGA data | 2) Prepare the data | 2) - PCAPAM50 vs PAM50 | 5. Citations