BridgeRResultChecker: BRIC-seq result checker

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

Description

BridgeRResultChecker returns several BRIC-seq result information. This function is used for checking the distribution of genome-wide RNA half-lives.

Usage

BridgeRResultChecker(inputFile, group = c("Control", "Knockdown"),
  hour = c(0, 1, 2, 4, 8, 12), inforColumn = 4, save = T,
  outputPrefix = "BridgeR_9")

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.
save	Whether to save the output fig file.
outputPrefix	The prefix for the name of the output.

Value

list object about ggplot2 fig data.

Examples

library(data.table)
normalized_table <- 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_table,
                                              group = group,
                                              hour = hour,
                                              save = FALSE)
pvalue_table <- BridgeRPvalueEvaluation(halflife_table,
                                        group = group,
                                        hour = hour,
                                        save = FALSE)
result_fig <- BridgeRResultChecker(pvalue_table,
                                   save = FALSE)

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