In danielschw188/Revelio:

library(Revelio)
myData <- createRevelioObject(rawData = revelioTestData_rawDataMatrix,
                              cyclicGenes = revelioTestData_cyclicGenes)

myData <- getCellCyclePhaseAssignInformation(dataList = myData)

myData <- getPCAData(dataList = myData,
                     boolPlotResults = TRUE)

myData <- getOptimalRotation(dataList = myData,
                             boolPlotResults = TRUE)

normalizedDataWithoutCCEffects <- removeCCEffects(dataList = myData)

myData <- getVelocityMatrix(dataList = myData,
                            rawIntronicData = revelioTestData_rawIntronicMatrix)

myData <- getPCAData(dataList = myData,
                     boolPlotResults = FALSE)
myData <- getOptimalRotation(dataList = myData,
                             boolPlotResults = TRUE)

myData <- getExtrapolatedStateInDCSpace(dataList = myData)

myData <- getVelocityGridCC(dataList = myData,
                            sigma = 0.6,
                            numberOfGridPointsOneSide = 20,
                            boolPlotResults = TRUE)

myData <- plotVelocityOnAveragedTrajectory(dataList = myData,
                                           numberOfAnchors = 10)

myData <- getVelocityGridAlongThirdDimensions(dataList = myData,
                                              whichThirdDimension = 3,
                                              sigma = 1.5,
                                              numberOfGridPointsOneSide = 20,
                                              boolPlotResults = TRUE)

danielschw188/Revelio documentation built on April 30, 2021, 1:02 p.m.