bridger2 (version 0.1.0)

BridgeRCore: BridgeR basic function for calculating RNA half-life from BRIC-seq data

Description

BridgeRCore is a basic function for calculating RNA half-life BRIC-seq data and a wrapper of the other individual bridger2 functions.

Usage

BridgeRCore(inputFile, inforColumn = 4, group = c("Control", "Knockdown"), hour = c(0, 1, 2, 4, 8, 12), RPKMcutoff = 0.1, cutoffBelow = 0.1, YMin = -2, YMax = 2, downsamplingFig = 0.2, makeFig = FALSE, cutoffQuantile = 0.975, inforHKGenesRow = "symbol", HKGenes = c("GAPDH", "PGK1", "PPIA", "ENO1", "ATP5B", "ALDOA"), CutoffTimePointNumber = 4, R2_criteria = 0.9, TimePointRemoval1 = c(1, 2), TimePointRemoval2 = c(8, 12), ThresholdHalfLife1 = 3, ThresholdHalfLife2 = 12, save = TRUE, outputPrefix = "BridgeR", normalization = "default", method = "default")

Arguments

inputFile

The vector of tab-delimited matrix file.

inforColumn

The number of information columns.

group

The vector of group names.

hour

The vector of time course about BRIC-seq experiment.

RPKMcutoff

Cutoff value of RPKM at 0hr.

cutoffBelow

Cutoff value of RPKM at all time points.

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.#' @param save Whether to save the output matrix file.

inforHKGenesRow

The column number of house-keeping gene information.

HKGenes

The vector of house-keeping genes.

CutoffTimePointNumber

The number of minimum time points for calc.

R2_criteria

The cutoff of R2 for R2 selection.

TimePointRemoval1

The candicate_1 of time point removal.

TimePointRemoval2

The candicate_2 of time point removal.

ThresholdHalfLife1

The cutoff of TimePointRemoval1.

ThresholdHalfLife2

The cutoff of TimePointRemoval2.

save

Whether to save the output matrix file.

outputPrefix

The prefix for the name of the output.

normalization

select "default" (percentile method) or "house_keeping_genes"

method

select "default" (R2 selection/1st-order) or "3models".

Value

data.table object including RNA half-life, R2 and the selected fitting model.

Examples

halflife_table <- BridgeRCore(RNA_halflife_comparison[1:30,],
                              save = FALSE)
halflife_table <- BridgeRCore(RNA_halflife_comparison_HK[177:206],
                              save = FALSE,
                              normalization = "house_keeping_genes",
                              method = "3models")