BridgeRNormalization: Calculate the normalized RPKM for BRIC-seq dataset.

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

Description

BridgeRNormalization calculates the normalized RPKM values.

Usage

BridgeRNormalization(inputFile, normFactorFile, group = c("Control",
  "Knockdown"), hour = c(0, 1, 2, 4, 8, 12), inforColumn = 4, save = T,
  outputPrefix = "BridgeR_4")

Arguments

inputFile	The vector of tab-delimited matrix file.
normFactorFile	The vector of tab-delimited normalization factor file.
group	The vector of group names.
hour	The vector of time course about BRIC-seq experiment.
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 normalized 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)
rpkm_list <- BridgeRDataSetFromMatrix(inputFile = rpkm_matrix,
                                      group = group,
                                      hour = hour,
                                      cutoff = 0.1,
                                      inforColumn = 4,
                                      save = FALSE)
raw_table <- rpkm_list[[1]]
test_table <- rpkm_list[[2]]
factor_table <- BridgeRNormalizationFactors(test_table,
                                            save = FALSE)
normalized_table <- BridgeRNormalization(test_table,
                                         factor_table,
                                         save = FALSE)

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