bridger2 (version 0.1.0)

BridgeRGrubbsTest: RNA half-life Grubbs test.

Description

BridgeRGrubbsTest calculates the p-value for each gene using grubbs test. The estimation is based on the standard deviation of RNA half-lives in control conditions.

Usage

BridgeRGrubbsTest(controlFile, compFile, hour = c(0, 1, 2, 4, 8, 12), controlGroup = c("CTRL_PUM1", "CTRL_PUM2", "CTRL_DKD"), inforColumn = 4, compIndex = 2, save = T, outputPrefix = "BridgeR_8")

Arguments

controlFile

The dataframe of halflife table.

compFile

The dataframe of RPKM table.

hour

The vector of time course about BRIC-seq experiment.

controlGroup

The vector of group names.

inforColumn

The number of information columns.

compIndex

The number of information columns.

save

Whether to save the output matrix file.

outputPrefix

The prefix for the name of the output.

Value

data.table object about Grabbs test result.

Examples

group <- c("Control", "Knockdown")
hour <- c(0, 1, 2, 4, 8, 12)
half_sd_table <- CalcHalflifeDeviation(halflife_table,
                                       RNA_halflife_grubbs_test,
                                       group = c("CTRL_1",
                                                 "CTRL_2",
                                                 "CTRL_3"),
                                       save = FALSE)
grubbs_table <- BridgeRGrubbsTest(half_sd_table,
                                  halflife_table,
                                  compIndex = 4,
                                  controlGroup = c("CTRL_1",
                                                   "CTRL_2",
                                                   "CTRL_3"),
                                  save = FALSE)