An R library for comprehensive BRIC-seq data analysis tool.
BridgeR library was made under R version 3.2.2.
##Dependencies (Required R libraries)
data.table
ggplot2
shiny
BSDA
##Install ###Linux
sudo R CMD INSTALL BridgeR
###Windows (1) Update the path variables on your Windows computer(64-bit)
C:\Program Files\R\R-3.2.2\bin
(2) Install BridgeR library on Command Prompt
R CMD INSTALL BridgeR
##Example (1) Calculate RNA half-life from your BRIC-seq dataset and compare RNA half-life bwtween two conditions.
library(BridgeR)
files <- c("Control.fpkm_table",
"Knockdown.fpkm_table")
hour <- c(0,1,2,4,8,12)
group <- c("Control","Knockdown")
BridgeRCore(InputFiles=files,
InforColumn=4,
group=group,
hour=hour,
SelectNormFactor=T,
CutoffDataPointNumber = 4,
CutoffDataPoint1 = c(1,2),
CutoffDataPoint2 = c(8,12),
ThresholdHalfLife = c(8,12),
ModelMode="R2_selection")
BridgeRCompare(InputFile="BridgeR_5C_HalfLife_calculation_R2_selection.txt",
InforColumn=4,
group=group,
hour=hour,
ComparisonFile=group,
CutoffDataPointNumber = 4,
ModelMode="R2_selection",
Calibration=F)
(2) Draw RNA decay curve predicted from your BRIC-seq dataset.
library(BridgeR)
RPKM_ctrl <- "Control.fpkm_table"
RPKM_kd <- "Knockdown.fpkm_table"
Normalized_data <- "BridgeR_5C_HalfLife_calculation_R2_selection.txt"
group <- c("Control","Knockdown")
hour <- c(0,1,2,4,8,12)
BridgeReport(filename1=RPKM_ctrl,
filename2=RPKM_kd,
filename3=Normalized_data,
group=group,
hour=hour,
ComparisonFile=group,
SearchRow = "symbol",
InforColumn = 4,
Color = c("black","red"),
CutoffDataPoint1 = c(1,2),
CutoffDataPoint2 = c(8,12))