BridgeRCustom: Custom 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 your custom normalization factor such as the RPKM of Luciferase.

BridgeRCustom(YourNormFactor, 
              SelectNormFactor=F,
              InputFiles, 
              InforColumn=4,
              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")

`YourNormFactor`	File pass: tab-delimited text about normalization factor for each sample
`SelectNormFactor`	Bool(True or False)
`InputFiles`	Vector
`InforColumn`	Integer
`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 your custom normalization factor such as the RPKM of Luciferase.

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.
#mynf <- "Luciferase2_Rel_RPKM.txt"
#files <- c("Control_genes_RefSeq_result_mRNA.fpkm_table",
#           "Knockdown1_genes_RefSeq_result_mRNA.fpkm_table",
#           "Knockdown2_genes_RefSeq_result_mRNA.fpkm_table")
#group <- c("Control","knockdown1","knockdown2")
#hour <- c(0,1,2,4,8,12)

#BridgeRCustom(YourNormFactor=mynf, InputFiles=files, group=group, hour=hour)

## The function is currently defined as
function (YourNormFactor, 
                          InputFiles, 
                          SelectNormFactor=F,
                          InforColumn=4, 
                          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") 
{
}