Check the validity of a compData result object

Share:

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

1

Arguments

object

A compData object

Author(s)

Charlotte Soneson

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.