bridger2 (version 0.1.0)

BridgeRDatasetChecker: BRIC-seq Dataset checker

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)