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bridger2 (version 0.1.0)

BridgeRDataSetFromRaw: Calculate relative RPKM expression from raw data.

Description

BridgeRDataSetFromRaw calculates the relative RPKM values compared with 0hr, importing tab-delimited txt file.

Usage

BridgeRDataSetFromRaw(inputFile, group = c("Control", "Knockdown"), hour = c(0, 1, 2, 4, 8, 12), cutoff = 0.1, cutoffBelow = 0.1, inforColumn = 4, save = T, outputPrefix = "BridgeR_1")

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.
cutoff
Cutoff value of RPKM at 0hr.
cutoffBelow
Cutoff value of RPKM at all time points.
inforColumn
The number of information columns.
save
Whether to save the output matrix file.
outputPrefix
The prefix for the name of the output.

Value

data.table object about relative RPKM values.