BridgeRDataSetFromMatrix {bridger2}

Calculate relative RPKM expression from data.table format.

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)