run_reporter: Run the main reporting pipeline.

In bioinformatist/LncPipeReporter: Automatically Aggregating and Summarizing lncRNA Analysis Results for Interactive Report

Description

Run the main reporting pipeline.

Usage

run_reporter(input = system.file(file.path("extdata", "demo_results"), package
  = "LncPipeReporter"), output = "reporter.html",
  output_dir = path.expand("~/LncPipeReports"), de.method = "edger",
  theme = "npg", cdf.percent = 10, max.lncrna.len = 10000,
  min.expressed.sample = 50, ask = FALSE)

Arguments

input	absolute path of input directory (results of up-stream analysis).
output	index file name (In HTML format).
output_dir	output directory (who holds all results and dependencies).
de.method	which method should be used to perform differential expression analysis? Could be 'edger'(default), 'noiseq' or 'deseq2'.
theme	journal palette applied to all plots supplied by package ggsci.
cdf.percent	percentage of values to display when calculating coding potential.
max.lncrna.len	maximum length of lncRNAs to display when calculating distribution (percentage).
min.expressed.sample	minimal percentage of expressed samples (percentage).
ask	need set parameters with graphical user-interface in browser?

Details

The function call a R markdown script internally by rmarkdown::render. There're also default paramter values in the script – sometimes if the user try run it manually in RStudio, knitr will bring him/her a graphical interface to choose/fill the value of paramters. Also you can use statement like rmarkdown::render('./reporter.Rmd', params = 'ask') to call the interface in browser.

Value

None

Examples

# Below takes too long time for running, so ignore them in R CMD check.
run_reporter()
run_reporter(ask = TRUE)
run_reporter(input = system.file(paste0("extdata", .Platform$file.sep, "demo_results"),
             package = "LncPipeReporter"),
             output = 'reporter.html', theme = 'npg', cdf.percent = 10,
             max.lncrna.len = 10000, min.expressed.sample = 50, ask = FALSE)

bioinformatist/LncPipeReporter documentation built on May 28, 2019, 7:11 p.m.