BridgeRDataSetFromMatrix: Calculate relative RPKM expression from data.table format.

In bridger2: Genome-Wide RNA Degradation Analysis Using BRIC-Seq Data

Description

BridgeRDataSetFromMatrix calculates the relative RPKM values compared with 0hr, importing data.table format.

Usage

BridgeRDataSetFromMatrix(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.

Examples

library(data.table)
rpkm_matrix <- data.table(gr_id = c(8, 9, 14),
                          symbol = c("AAAS", "AACS", "AADAT"),
                          accession_id = c("NM_015665", "NM_023928", "NM_182662"),
                          locus = c("chr12", "chr12", "chr4"),
                          CTRL_1_0h = c(41, 5, 5),
                          CTRL_1_1h = c(48, 7, 6),
                          CTRL_1_2h = c(56, 10, 6),
                          CTRL_1_4h = c(87, 12, 10),
                          CTRL_1_8h = c(124, 20, 11),
                          CTRL_1_12h = c(185, 22, 15),
                          gr_id = c(8, 9, 14),
                          symbol = c("AAAS", "AACS", "AADAT"),
                          accession_id = c("NM_015665", "NM_023928", "NM_182662"),
                          locus = c("chr12", "chr12", "chr4"),
                          KD_1_0h = c(21, 10, 3),
                          KD_1_1h = c(33, 11, 3),
                          KD_1_2h = c(42, 15, 4),
                          KD_1_4h = c(60, 20, 5),
                          KD_1_8h = c(65, 37, 6),
                          KD_1_12h = c(70, 42, 6))
group <- c("Control", "Knockdown")
hour <- c(0, 1, 2, 4, 8, 12)
test_table <- BridgeRDataSetFromMatrix(inputFile = rpkm_matrix,
                                       group = group,
                                       hour = hour,
                                       cutoff = 0.1,
                                       inforColumn = 4,
                                       save = FALSE)

bridger2 documentation built on May 2, 2019, 8:14 a.m.