getPredictionSimplifiedModelForEachGene: Get predictions from estimated kinetic rates using simplified...

In haiyueliu/Eskrate: Estimate time-dependent RNA kinetics

Get predictions from estimated kinetic rates using simplified model

Description

Get predictions from estimated kinetic rates using simplified model

Usage

getPredictionSimplifiedModelForEachGene(
  parameterDF,
  boolCheckedInputCCTimeHasNoDuplicates = FALSE,
  boolCalculateInMinutes = TRUE,
  totalTimeOfOneCCInHours = 19.33,
  totalTimeOfOneCCInMinutes = 19.33 * 60,
  lengthToSimulatePerRoundInHours = 5,
  lengthToSimulatePerRoundInMinutes = 5 * 60,
  toleranceMature = 1,
  maximumNumberOfPeriodsToSimulate = 10,
  bytePrecisionForLargerNumbersToUse = 60
)

Arguments

parameterDF	a data frame with transcription (alpha) and degradation (gamma) rate for each gene at each cell cycle time
boolCheckedInputCCTimeHasNoDuplicates	logical statement (default: TRUE)
boolCalculateInMinutes	logical 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)
lengthToSimulatePerRoundInHours	numeric (default: 5)
lengthToSimulatePerRoundInMinutes	numeric (default: 5*60)
toleranceMature	numeric (default: 1)
maximumNumberOfPeriodsToSimulate	numeric (default: 10)
bytePrecisionForLargerNumbersToUse	numeric (default: 60)

Value

a data frame with predicted gene expression for both labeled and unlabeled mature RNAs at each cell cycle time.

Examples

data_predicted <- getPredictionSimplifiedModelForEachGene(parameterDF = data_rate)
p_u' = rep(NA, dim(parameterDF)[1]),
p_total' = rep(NA, dim(parameterDF)[1]),
p_u' = rep(NA, dim(parameterDF)[1]),
p_total' = rep(NA, dim(parameterDF)[1]),
p_u' = rep(NA, dim(parameterDF)[1]),
p_total' = rep(NA, dim(parameterDF)[1]),
p_u' = rep(NA, length(associatedtValuesThisLoop)),
p_total' = rep(NA, length(associatedtValuesThisLoop)),
p_u' = rep(NA, length(associatedtValuesThisLoop)),
p_total' = rep(NA, length(associatedtValuesThisLoop)),

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