BridgeReport {bridger2} | R Documentation |
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)
[Package bridger2 version 0.1.0 Index]