BridgeRNormalizationFactorsHK {bridger2}

Calculate normalization factors from house-keeping genes.

Description

BridgeRNormalizationFactorsHK calculates the normalization factors from house-keeping genes.

Usage

BridgeRNormalizationFactorsHK(inputFile, group = c("Control", "Knockdown"),
  hour = c(0, 1, 2, 4, 8, 12), inforColumn = 4,
  inforHKGenesRow = "symbol", HKGenes = c("GAPDH", "PGK1", "PPIA", "ENO1",
  "ATP5B", "ALDOA"), save = T, factorOutputPrefix = "BridgeR_3")

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.

inforColumn

The number of information columns.

inforHKGenesRow

The column number of house-keeping gene information.

HKGenes

The vector of house-keeping genes.

save

Whether to save the output matrix file.

factorOutputPrefix

The prefix for the name of factor output.

Value

data.table object about normalization factor calculated by house-keeping genes.

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 <- BridgeRNormalizationFactorsHK(test_table,
                                              save = FALSE)