BridgeRDatasetChecker: BRIC-seq Dataset checker

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

Description

BridgeRDatasetChecker returns several BRIC-seq dataset information. This function is used for checking your BRIC-seq dataset quality.

Usage

BridgeRDatasetChecker(inputFile, group = c("Control", "Knockdown"),
  hour = c(0, 1, 2, 4, 8, 12), inforColumn = 4, percentile = c(0.99, 0.95,
  0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, 0.05), save = T,
  outputPrefix = "BridgeR_2_raw")

Arguments

inputFile	Input matrix object.
group	The vector of group names.
hour	The vector of time course about BRIC-seq experiment.
inforColumn	The number of information columns.
percentile	Percentile numbers.
save	Whether to save the output fig file.
outputPrefix	The prefix for the name of the output.

Value

list object about ggplot2 fig data.

Examples

library(data.table)
normalized_table <- 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(1.00, 1.00, 1.00),
                               CTRL_1_1h = c(1.00, 0.86, 0.96),
                               CTRL_1_2h = c(1.00, 0.96, 0.88),
                               CTRL_1_4h = c(1.00, 0.74, 0.85),
                               CTRL_1_8h = c(1.00, 0.86, 0.68),
                               CTRL_1_12h = c(1.01, 0.65, 0.60),
                               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(1.00, 1.00, 1.00),
                               KD_1_1h = c(1.01, 0.73, 0.71),
                               KD_1_2h = c(1.01, 0.77, 0.69),
                               KD_1_4h = c(1.01, 0.72, 0.67),
                               KD_1_8h = c(1.01, 0.64, 0.38),
                               KD_1_12h = c(1.00, 0.89, 0.63))
group <- c("Control", "Knockdown")
hour <- c(0, 1, 2, 4, 8, 12)
fig_list_norm <- BridgeRDatasetChecker(inputFile = normalized_table,
                                       save = FALSE)

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