BridgeRCore: BridgeR basic function for calculating RNA half-life from...
In bridger2: Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

Description Usage Arguments Value Examples

BridgeRCore is a basic function for calculating RNA half-life BRIC-seq data and a wrapper of the other individual bridger2 functions.

BridgeRCore(inputFile, inforColumn = 4, group = c("Control", "Knockdown"),
  hour = c(0, 1, 2, 4, 8, 12), RPKMcutoff = 0.1, cutoffBelow = 0.1,
  YMin = -2, YMax = 2, downsamplingFig = 0.2, makeFig = FALSE,
  cutoffQuantile = 0.975, inforHKGenesRow = "symbol", HKGenes = c("GAPDH",
  "PGK1", "PPIA", "ENO1", "ATP5B", "ALDOA"), CutoffTimePointNumber = 4,
  R2_criteria = 0.9, TimePointRemoval1 = c(1, 2), TimePointRemoval2 = c(8,
  12), ThresholdHalfLife1 = 3, ThresholdHalfLife2 = 12, save = TRUE,
  outputPrefix = "BridgeR", normalization = "default", method = "default")

`inputFile`	The vector of tab-delimited matrix file.
`inforColumn`	The number of information columns.
`group`	The vector of group names.
`hour`	The vector of time course about BRIC-seq experiment.
`RPKMcutoff`	Cutoff value of RPKM at 0hr.
`cutoffBelow`	Cutoff value of RPKM at all time points.
`YMin`	Y-axis min.
`YMax`	Y-axis max.
`downsamplingFig`	the factor for downsampling.
`makeFig`	Whether to save the figure of normalization factor.
`cutoffQuantile`	cutoff value of quantile.#' @param save Whether to save the output matrix file.
`inforHKGenesRow`	The column number of house-keeping gene information.
`HKGenes`	The vector of house-keeping genes.
`CutoffTimePointNumber`	The number of minimum time points for calc.
`R2_criteria`	The cutoff of R2 for R2 selection.
`TimePointRemoval1`	The candicate_1 of time point removal.
`TimePointRemoval2`	The candicate_2 of time point removal.
`ThresholdHalfLife1`	The cutoff of TimePointRemoval1.
`ThresholdHalfLife2`	The cutoff of TimePointRemoval2.
`save`	Whether to save the output matrix file.
`outputPrefix`	The prefix for the name of the output.
`normalization`	select "default" (percentile method) or "house_keeping_genes"
`method`	select "default" (R2 selection/1st-order) or "3models".

data.table object including RNA half-life, R2 and the selected fitting model.

halflife_table <- BridgeRCore(RNA_halflife_comparison[1:30,],
                              save = FALSE)
halflife_table <- BridgeRCore(RNA_halflife_comparison_HK[177:206],
                              save = FALSE,
                              normalization = "house_keeping_genes",
                              method = "3models")