BridgeRHKGenes: Classic 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 the RPKM of house-keeping genes.

BridgeRHKGenes(InputFiles,
                           InforColumn=4, 
                           InforHKGenes=2, 
                           HKGenes=c("GAPDH","PGK1","PPIA","ENO1","ATP5B","ALDOA"), 
                           group, 
                           hour, 
                           RPKMcutoff=0.1,
                           CutoffDataPointNumber = 4,
                           CutoffDataPoint1 = c(1,2),
                           CutoffDataPoint2 = c(8,12),
                           ThresholdHalfLife = c(8,12),
                           CutoffRelExp=0.001,
                           ModelMode="R2_selection")

`InputFiles`	Vector
`InforColumn`	Integer
`InforHKGenes`	Integer
`HKGenes`	String(gene_name)
`group`	Vector(string)
`hour`	Vector(number)
`RPKMcutoff`	Float
`CutoffDataPointNumber`	Integer
`CutoffDataPoint1`	Vector(Integer or float)
`CutoffDataPoint2`	Vector(Integer or float)
`ThresholdHalfLife`	Vector(Integer or float)
`CutoffRelExp`	Float
`ModelMode`	Bool(True or False)

RNA half-life for each gene is calculated using the RPKM of house-keeping genes.

text files and fig files

2015-11-05

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, 
                           InforHKGenes=2, 
                           HKGenes=c("GAPDH","PGK1","PPIA","ENO1","ATP5B","ALDOA"), 
                           group, 
                           hour, 
                           RPKMcutoff=0.1,
                           CutoffDataPointNumber = 4,
                           CutoffDataPoint1 = c(1,2),
                           CutoffDataPoint2 = c(8,12),
                           ThresholdHalfLife = c(8,12),
                           CutoffRelExp=0.001,
                           ModelMode="R2_selection") 
{
}