check_compData_results: Check the validity of a 'compData' result object

In csoneson/compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Check the validity of a compData result object

Description

Check the validity of a compData object containing differential expression results. An object that passes the check can be used as the input for the method comparison functions in compcodeR.

Usage

check_compData_results(object)

Arguments

object

A compData object

Author(s)

Charlotte Soneson

Examples

tmpdir <- normalizePath(tempdir(), winslash = "/")
mydata <- generateSyntheticData(dataset = "mydata", n.vars = 1000, 
                                samples.per.cond = 5, n.diffexp = 100,
                                output.file = file.path(tmpdir, "mydata.rds"))
## Check an object without differential expression results
check_compData_results(mydata)

runDiffExp(data.file = file.path(tmpdir, "mydata.rds"), 
           result.extent = "voom.limma", 
           Rmdfunction = "voom.limma.createRmd", 
           output.directory = tmpdir, norm.method = "TMM")
resdata <- readRDS(file.path(tmpdir, "mydata_voom.limma.rds"))
## Check an object containing differential expression results
check_compData_results(resdata)

csoneson/compcodeR documentation built on Oct. 25, 2023, 1:28 a.m.