BridgeRHalfLifeCalc3models: Calculate RNA half-life for each gene using 3model method.

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

Description

BridgeRHalfLifeCalc3models calculates RNA half-life for each gene using 3 models methods (older version).

Usage

BridgeRHalfLifeCalc3models(inputFile, group = c("Control", "Knockdown"),
  hour = c(0, 1, 2, 4, 8, 12), inforColumn = 4, CutoffTimePointNumber = 4,
  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.
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 <- BridgeRHalfLifeCalc3models(normalized_rpkm_matrix,
                                             group = group,
                                             hour = hour,
                                             save = FALSE)

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