BridgeRPvalueEvaluation {bridger2}

Calculate Fold-change of RNA half-life and p-value.

Description

BridgeRPvalueEvaluation calculates the fold-change of RNA half-life and p-value between two conditions.

Usage

BridgeRPvalueEvaluation(inputFile, group = c("Control", "Knockdown"),
  hour = c(0, 1, 2, 4, 8, 12), comparisonFile = c("Control", "Knockdown"),
  inforColumn = 4, CutoffTimePointNumber = 4, calibration = FALSE,
  save = TRUE, outputPrefix = "BridgeR_6")

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.

comparisonFile

The vector of group names.

inforColumn

The number of information columns.

CutoffTimePointNumber

The number of minimum time points for calc.

calibration

Calibration of RNA half-life.

save

Whether to save the output matrix file.

outputPrefix

The prefix for the name of the output.

Value

data.table object about Fold-change of RNA half-lives, p-value.

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)
pvalue_table <- BridgeRPvalueEvaluation(halflife_table,
                                        group = group,
                                        hour = hour,
                                        save = FALSE)