Man pages for dsherma7/PolyploidDosageCalling
Calls the Dosage From Tetraploid qPCR Data (CT/RQ Values)
| AllPossibleCalSamples | Determines All Calibration Sample Subsets |
| BuildSummary | Gets the Predicted Dosage from Combined Dosage Calls |
| CallAllPA | Runs CallPA() on all files in a directory |
| CallDosage | Calls dosage for a given input file |
| CallDosageAPI | Main Dosage Calling Function for the API |
| CallPA | Calls Presence/Absence for a given input file |
| CallSinglePA | Determines if a Given Assay is Present in a Sample |
| ChooseClosestCluster | Determine Closest Cluster to Sample |
| CombineDosages | Combine Each of the Models |
| ComputeScores | Measures the Accuracy of a Model vs. Control Dosages |
| ConvertList | Converts List into data Frame |
| CountSections | Helper Function for Manual Call |
| distance | Distance Measure |
| DosageOfAllCombos | Get the Dosage for All Combinations of Controls |
| DosageOfGivenCombo | Find the Dosage Given a Subset of Controls |
| GetConf | Measures the Confidence in Prediction |
| GetDosage | Linear Regression on PCR Variables |
| GetDosageForSinglePlate | Linear Model on a Single Plate |
| GetManualCall | Performs a Simulated Manual Call |
| GetPCH | Print Output Graph |
| GetPredicted | Gets the Predicted Dosage from Combined Dosage Calls |
| GetSemiSuperClusters | Driver Function for Calling Semi-Supervised Clustering... |
| isOutlier | Determines if Controls are Outliers |
| LoadAllData | Loads All Data Sets |
| MakeSwaps | Swaps any changed sample values |
| ManualCall | Simulated Manual Dosage Call |
| ManualCall.Trials | Runs Multiple Iterations of Manual Call |
| MeasureConfidence | Measures the Confidence of An AllComboFit Output |
| MyClustering | Semi-Supervised Clustering Algorithm |
| ParsePAComments | Determines if a Given Assay is Present in a Sample |
| PlotPA | Print Output for Presence/Absence Calling |
| PrintBarGraph | Print Output Bar/Histogram Graph |
| PrintGraph | Print Output Graph |
| RemoveDuplicateNames | Removes Duplicated Names in List |
