calculateKineticsForEachGene: Calculate time-dependent alpha (transcription rate) and gamma...

In haiyueliu/Eskrate: Estimate time-dependent RNA kinetics

Calculate time-dependent alpha (transcription rate) and gamma (degradation rate) for each gene using observed gene expression of m_u, m_total

Description

Calculate time-dependent alpha (transcription rate) and gamma (degradation rate) for each gene using observed gene expression of m_u, m_total

Usage

calculateKineticsForEachGene(
  observedData,
  boolCalculateInMinutes = TRUE,
  totalTimeOfOneCCInHours = 19.33,
  totalTimeOfOneCCInMinutes = 19.33 * 60,
  numberOfSplineAnchors = 20,
  boolSetBetaConstantBeforeAlphaEstimate = TRUE,
  ignoreOutliers = TRUE,
  boolUseCPM = TRUE,
  smallestLabelingTime = NULL
)

Arguments

boolCalculateInMinutes	logic statement (default: TRUE)
totalTimeOfOneCCInHours	numeric total cell cycle time in hours (default: 19.33)
totalTimeOfOneCCInMinutes	numeric total cell cycle time in minutes (default: 19.33*60)
numberOfSplineAnchors	number of spline anchors used for smoothing profiles (default: 20)
boolSetBetaConstantBeforeAlphaEstimate	logic statement (default: TRUE)
ignoreOutliers	logic statement (default: TRUE)
boolUseCPM	logic statement (default: TRUE)
smallestLabelingTime	a number the smallest metabolic labeling time (default: 15)
observedCounts	data frame

Value

a data frame with kinetic rates of transcription (alpha) and degradation (gamma) for each gene at each cell cycle time

Examples

data_rate <- calculateKineticsForEachGene(observedCounts, smallestLabelingTime = 15)

haiyueliu/Eskrate documentation built on Sept. 3, 2023, 3:33 p.m.