bridger2 (version 0.1.0)

BridgeRResultChecker: BRIC-seq result checker

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)