BridgeRNormalizationFactors: Calculate normalization factors for BRIC-seq datasets.

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

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)

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