reportFuse: reportFuse

Description Usage Arguments Details Value Examples

View source: R/reportFuse.R

Description

reportFuse

Usage

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reportFuse(
  out_annofuse,
  project_id = "projectID",
  input_rmd = NULL,
  output_file = "my_first_annoFuse_report.html",
  output_dir = tempdir(),
  output_format = NULL,
  force_overwrite = FALSE,
  knitr_show_progress = FALSE,
  open_after_creating = TRUE,
  ...
)

Arguments

out_annofuse

The character string specifying the location of the file output by the annoFuse pipeline.

project_id

A character string, which can be considered as an identifier for the set/session, and will be e.g. used in the title of the report created via [reportFuse()]

input_rmd

Character string with the path to the RMarkdown (.Rmd) file that will be used as the template for generating the report. Defaults to NULL, which will then use the one provided with the 'annoFuse' package.

output_file

Character string, specifying the file name of the output report. The file name extension must be either '.html' or '.pdf', and consistent with the value of 'output_format'.

output_dir

Character, defining the path to the output directory where the report will be generated. Defaults to the temp directory ('tempdir()').

output_format

The format of the output report. Either 'html_document' or 'pdf_document'. The file name extension of 'output_file' must be consistent with this choice. Can also be left empty and determined accordingly.

force_overwrite

Logical, whether to force overwrite an existing report with the same name in the output directory. Defaults to FALSE.

knitr_show_progress

Logical, whether to display the progress of 'knitr' while generating the report. Defaults to FALSE.

open_after_creating

Logical, whether to open the report in the default browser after being generated. Defaults to TRUE.

...

Other arguments that will be passed to [rmarkdown::render()].

Details

When 'reportFuse' is called, a RMarkdown template file could be copied into the output directory, and [rmarkdown::render()] will be called to generate the final report.

As a default template, 'reportFuse' uses the one delivered together with the 'annoFuse' package. Experienced users can take that as a starting point to further edit and customize.

Value

Generates a fully fledged report in the 'output_dir' directory, called 'output_file' and returns (invisibly) the name of the generated report.

Examples

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out_annofuse <- system.file("extdata", "PutativeDriverAnnoFuse.tsv", package = "annoFuseData")
## Not run: 
reportFuse(out_annofuse = out_annofuse)

## End(Not run)

d3b-center/annoFuse documentation built on March 11, 2021, 9:05 p.m.