BridgeRDataSetFromRaw {bridger2}

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.