reportFuse: reportFuse

In d3b-center/annoFuse: annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

reportFuse

Description

reportFuse

Usage

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

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 Oct. 2, 2024, 4:17 a.m.