run_reporter: Run the main reporting pipeline.

Description Usage Arguments Details Value Examples

View source: R/run_reporter.R

Description

Run the main reporting pipeline.

Usage

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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

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# 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/LncPipe-Reporter documentation built on Nov. 20, 2018, 8:18 p.m.