bridger2 (version 0.1.0)

BridgeRNormalizationFactors: Calculate normalization factors for BRIC-seq datasets.

Description

BridgeRNormalizationFactors calculates the normalization factors for BRIC-seq datasets.

Usage

BridgeRNormalizationFactors(inputFile, group = c("Control", "Knockdown"), hour = c(0, 1, 2, 4, 8, 12), inforColumn = 4, save = T, YMin = -2, YMax = 2, downsamplingFig = 0.2, makeFig = FALSE, cutoffQuantile = 0.975, figOutputPrefix = "BridgeR_3_fig", 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.

save

Whether to save the output matrix file.

YMin

Y-axis min.

YMax

Y-axis max.

downsamplingFig

the factor for downsampling.

makeFig

Whether to save the figure of normalization factor.

cutoffQuantile

cutoff value of quantile.

figOutputPrefix

The prefix for the name of figure output.

factorOutputPrefix

The prefix for the name of factor output.

Value

data.table object about normalization factors calculated by quantile method.

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)