Man pages for PriceLab/FPML
Footprint Machine Learning
| addTSSDistance | Add Transcription Start Site Distance |
| annotateFootprintData | Annotate the Footprint Data |
| buildBoostedModel | Build a Gradient Boosted Model |
| buildLinearModels | Build a Linear Models |
| constructLymphoblastDataset | Construct the Lymphoblast Datast |
| createBiasOneMotif | Create a biased training set for one motif |
| createMotifClassMap | Create Motif Class Map |
| createTfDf | Pull all FIMO Motifs for a Given TF |
| createThresholdPlot | Create a threshold plot |
| createTruthPlot | Create the "truth plot" |
| extractMaxMCC | Extract the Maximum MCC Values |
| FPML-package | Footprint Machine Learning |
| getGCContent | Add GC content |
| joinModelData | Join the Seed 16 and Seed 20 Data |
| make.pred.df.from.glm | Create a Data Frame of Predictions for ChIPseq Data Using a... |
| make.pred.df.from.model | Create a Data Frame of Predictions for ChIPseq Data Using a... |
| make.stats.df.from.preds | Create the "Stats" Data Frame from Prediction Data Frame |
| mapTFsToMotifs | Create a TF-Motif Map in List Form |
| mattcc | Compute Matthews Correlation Coefficient |
| mattcc.curve | Create Matthews Correlation Coefficient Data for Plotting |
| mergeFootprintsOneChrom | Merge Footprints for 1 Chromosome |
| mergeLymphoblastFootprints | Merge Footprints for Lymphoblast Data |
| plot.all.curve | Plot All Curves |
| plotImportanceMatrix | Plot the Importance Matrix for a Gradient Boosted Model |
| plot.mattcc.curve | Plot a Matthews Correlation Coefficient Curve |
| plot.precrecall.curve | Plot Precision-Recall Curve |
| plot.roc.curve | Plot ROC Curve |
| plotStatCurves | Make plots for MCC, ROC, and Prec-Rec |
| prepModelData | Prepare Dataset for Modeling |
| sampleTfDataset | Sample the FIMO/ChIPSeq Dataset |
