BridgeReport: Shinyapp reporting for drawing RNA decay curve.

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

Description

BridgeReport returns a shinyapp object to draw RNA decay curve. You can easily check RNA half-life and RNA decay fitting curve on your web browser.

Usage

BridgeReport(inputFile, group = c("Control", "Knockdown"), hour = c(0, 1, 2,
  4, 8, 12), comparisonFile = c("Control", "Knockdown"),
  searchRowName = "symbol", inforColumn = 4, color = c("black", "red"),
  TimePointRemoval1 = c(1, 2), TimePointRemoval2 = c(8, 12))

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.
searchRowName	Row name for searching.
inforColumn	The number of information columns.
color	color of line graph for two decay curve.
TimePointRemoval1	The candicate_1 of time point removal.
TimePointRemoval2	The candicate_2 of time point removal.

Value

shiny.appobj object for searching and showing RNA decay curve for each gene.

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,
                                        save = FALSE)
shiny_test <- BridgeReport(pvalue_table)

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