BridgeRHalfLifeCalcR2Select: Calculate RNA half-life for each gene using R2 selection...

In bridger2: Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

Description

BridgeRHalfLifeCalcR2Select calculates RNA half-life for each gene using R2 selection method (default version).

Usage

BridgeRHalfLifeCalcR2Select(inputFile, group = c("Control", "Knockdown"),
  hour = c(0, 1, 2, 4, 8, 12), inforColumn = 4, CutoffTimePointNumber = 4,
  R2_criteria = 0.9, TimePointRemoval1 = c(1, 2), TimePointRemoval2 = c(8,
  12), ThresholdHalfLife1 = 3, ThresholdHalfLife2 = 12, save = T,
  outputPrefix = "BridgeR_5")

Arguments

inputFile	The vector of tab-delimited matrix file.
group	The vector of group names.
hour	The vector of time course about BRIC-seq experiment.
inforColumn	The number of information columns.
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.

Value

data.table object about RNA half-life, R2 and fitting model.

Examples

library(data.table)
normalized_rpkm_matrix <- data.table(gr_id = c(8, 9, 14),
                                     symbol = c("AAAS", "AACS", "AADAT"),
                                     accession_id = c("NM_015665", "NM_023928", "NM_182662"),
                                     locus = c("chr12", "chr12", "chr4"),
                                     CTRL_1_0h = c(1.00, 1.00, 1.00),
                                     CTRL_1_1h = c(1.00, 0.86, 0.96),
                                     CTRL_1_2h = c(1.00, 0.96, 0.88),
                                     CTRL_1_4h = c(1.00, 0.74, 0.85),
                                     CTRL_1_8h = c(1.00, 0.86, 0.68),
                                     CTRL_1_12h = c(1.01, 0.65, 0.60),
                                     gr_id = c(8, 9, 14),
                                     symbol = c("AAAS", "AACS", "AADAT"),
                                     accession_id = c("NM_015665", "NM_023928", "NM_182662"),
                                     locus = c("chr12", "chr12", "chr4"),
                                     KD_1_0h = c(1.00, 1.00, 1.00),
                                     KD_1_1h = c(1.01, 0.73, 0.71),
                                     KD_1_2h = c(1.01, 0.77, 0.69),
                                     KD_1_4h = c(1.01, 0.72, 0.67),
                                     KD_1_8h = c(1.01, 0.64, 0.38),
                                     KD_1_12h = c(1.00, 0.89, 0.63))
group <- c("Control", "Knockdown")
hour <- c(0, 1, 2, 4, 8, 12)
halflife_table <- BridgeRHalfLifeCalcR2Select(normalized_rpkm_matrix,
                                              group = group,
                                              hour = hour,
                                              save = FALSE)

bridger2 documentation built on May 2, 2019, 8:14 a.m.