Man pages for PriceLab/FPML
Footprint Machine Learning

addTSSDistanceAdd Transcription Start Site Distance
annotateFootprintDataAnnotate the Footprint Data
buildBoostedModelBuild a Gradient Boosted Model
buildLinearModelsBuild a Linear Models
constructLymphoblastDatasetConstruct the Lymphoblast Datast
createBiasOneMotifCreate a biased training set for one motif
createMotifClassMapCreate Motif Class Map
createTfDfPull all FIMO Motifs for a Given TF
createThresholdPlotCreate a threshold plot
createTruthPlotCreate the "truth plot"
extractMaxMCCExtract the Maximum MCC Values
FPML-packageFootprint Machine Learning
getGCContentAdd GC content
joinModelDataJoin the Seed 16 and Seed 20 Data
make.pred.df.from.glmCreate a Data Frame of Predictions for ChIPseq Data Using a...
make.pred.df.from.modelCreate a Data Frame of Predictions for ChIPseq Data Using a...
make.stats.df.from.predsCreate the "Stats" Data Frame from Prediction Data Frame
mapTFsToMotifsCreate a TF-Motif Map in List Form
mattccCompute Matthews Correlation Coefficient
mattcc.curveCreate Matthews Correlation Coefficient Data for Plotting
mergeFootprintsOneChromMerge Footprints for 1 Chromosome
mergeLymphoblastFootprintsMerge Footprints for Lymphoblast Data
plot.all.curvePlot All Curves
plotImportanceMatrixPlot the Importance Matrix for a Gradient Boosted Model
plot.mattcc.curvePlot a Matthews Correlation Coefficient Curve
plot.precrecall.curvePlot Precision-Recall Curve
plot.roc.curvePlot ROC Curve
plotStatCurvesMake plots for MCC, ROC, and Prec-Rec
prepModelDataPrepare Dataset for Modeling
sampleTfDatasetSample the FIMO/ChIPSeq Dataset
PriceLab/FPML documentation built on May 28, 2019, 2:25 p.m.