GetPredicted: Gets the Predicted Dosage from Combined Dosage Calls

In dsherma7/PolyploidDosageCalling: Calls the Dosage From Tetraploid qPCR Data (CT/RQ Values)

Description

Checks the different models' accuracy against the controls and then sets the predicted values to be the best model.

Usage

GetPredicted(df, Controls, Output.Dir, Target = "Assay1",
  Methods = c("Linear", "Multinomial", "Manual", "SemiSupervised",
  "QS.Dosage"), Console = F, LL.min = 0.5, nulliplex.thresh = 0.02)

Arguments

df	The dataset built from joining the results of each method specified in methods. Use CombineDosages
Controls	The Controls with Well information included
Output.Dir	The directory to print the resulting plots to. Uneccesary if Console=T.
Target	The target assay. This is used primarily to rename the "Predicted" and "Probability" columns to the correct names. The assay names Assay1,Assay1#,Assay1CN, Assay1 CN, etc. will all generate a column named Assay1# and Assay1#_Pr.
Methods	The different methods combined with CombineDosages. Must match df's column names for these predictions.
Console	Should the plots be printed to the console and not saved to Output.Dir? (Default=F).
LL.min	Any predictions with likelihood less than this will be ignored. Predictions with likelihood greater than this will be included in the final predictions weighted average. (Default=0.5)
nulliplex.thres	Final predictions with RQ < nulliplex.thresh will be set to nulliplex. Necessary the reaction fails for all nulliplex controls (very probable.). (Default = 0.2)
Controls	the list of Controls for the dataset df.

dsherma7/PolyploidDosageCalling documentation built on May 23, 2019, 6:06 p.m.