bridger2 (version 0.1.0)

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

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)