BridgeRCore: Default BRIC-seq data analysis pipeline
In Naoto-Imamachi/BridgeR: Comprehensive BRIC-seq data analysis tool

Description Usage Arguments Details Value Note Author(s) References Examples

RNA half-life for each gene is calculated using 99-97.5 percentile normalization.

BridgeRCore(InputFiles,
                        InforColumn=4,
                        group,
                        hour,
                        RPKMcutoff=0.1,
                        RelRPKMFig=F,
                        SelectNormFactor=T,
                        CutoffDataPointNumber = 4,
                        CutoffDataPoint1 = c(1,2),
                        CutoffDataPoint2 = c(8,12),
                        ThresholdHalfLife = c(8,12),
                        CutoffRelExp=0.001,
                        ModelMode="R2_selection")

`InputFiles`	Vector
`InforColumn`	Integer
`group`	Vector
`hour`	Vector(number)
`RPKMcutoff`	Float
`RelRPKMFig`	Bool(True or False)
`SelectNormFactor`	Bool(True or False)
`CutoffDataPointNumber`	Integer
`CutoffDataPoint1`	Vector(Integer)
`CutoffDataPoint2`	Vector(Integer)
`ThresholdHalfLife`	Vector(Integer)
`CutoffRelExp`	Float
`ModelMode`	Mode

RNA half-life for each gene is calculated Using 99-97.5 percentile normalization.

text files and fig files

2015-11-24

Naoto Imamachi

https://github.com/Naoto-Imamachi/BRIC-seq_data_analysis/tree/master/BridgeR

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (InputFiles,
                        InforColumn=4,
                        group,
                        hour,
                        RPKMcutoff=0.1,
                        RelRPKMFig=F,
                        SelectNormFactor=T,
                        CutoffDataPointNumber = 4,
                        CutoffDataPoint1 = c(1,2),
                        CutoffDataPoint2 = c(8,12),
                        ThresholdHalfLife = c(8,12),
                        CutoffRelExp=0.001,
                        ModelMode="R2_selection") 
{
}