summarizeSyntheticDataSet: Summarize a synthetic data set by some diagnostic plots

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

Description

Summarize a synthetic data set (generated by generateSyntheticData) by some diagnostic plots.

Usage

summarizeSyntheticDataSet(data.set, output.filename)

Arguments

data.set	A data set, either a compData object or a path to an .rds file where such an object is stored.
output.filename	The filename of the resulting html report (including the path).

Author(s)

Charlotte Soneson

Examples

tmpdir <- normalizePath(tempdir(), winslash = "/")
mydata.obj <- generateSyntheticData(dataset = "mydata", n.vars = 1000, 
                                    samples.per.cond = 5, n.diffexp = 100, 
                                    output.file = file.path(tmpdir, "mydata.rds"))
if (interactive()) {
  summarizeSyntheticDataSet(data.set = file.path(tmpdir, "mydata.rds"), 
                            output.filename = file.path(tmpdir, "mydata_check.html"))
}

Example output

Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Registered S3 method overwritten by 'gplots':
  method         from 
  reorder.factor gdata
Warning messages:
1: no DISPLAY variable so Tk is not available 
2: replacing previous import ‘gdata::reorder.factor’ by ‘gplots::reorder.factor’ when loading ‘compcodeR’ 

compcodeR documentation built on Nov. 10, 2020, 2 a.m.