bridger2 (version 0.1.0)

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

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)