bridger2 (version 0.1.0)

BridgeReport: Shinyapp reporting for drawing RNA decay curve.

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)