alevinQCReport: Generate alevin summary report
In alevinQC: Generate QC Reports For Alevin Output

Description Usage Arguments Details Value Author(s) Examples

Generate a report summarizing the main aspects of an alevin quantification run. The report generation assumes that alevin has been run with the –dumpFeatures flag to generate the necessary output files.

alevinQCReport(
  baseDir,
  sampleId,
  outputFile,
  outputDir = "./",
  outputFormat = NULL,
  showCode = FALSE,
  forceOverwrite = FALSE,
  knitrProgress = FALSE,
  quiet = FALSE,
  ignorePandoc = FALSE,
  customCBList = list(),
  ...
)

`baseDir`	Path to the output directory from the alevin run (should be the directory containing the `alevin` directory).
`sampleId`	Sample ID, will be used to set the title for the report.
`outputFile`	File name of the output report. The file name extension must be either `.html` or `.pdf`, and consistent with the value of `outputFormat`.
`outputDir`	Path to the output directory where the report will be generated.
`outputFormat`	The format of the output report. Either `"html_document"` or `"pdf_document"`. The file name extension of `outputFile` must be consistent with this choice.
`showCode`	Logical, whether to display the R code in the report.
`forceOverwrite`	Logical, whether to force overwrite an existing report with the same name in the output directory.
`knitrProgress`	Logical, whether to display the progress of `knitr` when generating the report.
`quiet`	Logical, whether to show progress messages.
`ignorePandoc`	Logical, determines what to do if `pandoc` or `pandoc-citeproc` is missing (if `Sys.which("pandoc")` or `Sys.which("pandoc-citeproc")` returns ""). If `ignorePandoc` is TRUE, only a warning is given. The figures will be generated, but not the final report. If `ignorePandoc` is FALSE (default), the execution stops immediately.
`customCBList`	Named list with custom set(s) of barcodes to provide summary statistics/plots for, in addition to the whitelists generated by alevin.
`...`	Other arguments that will be passed to `rmarkdown::render`.

When the function is called, a .Rmd template file will be copied into the output directory, and rmarkdown::render will be called to generate the final report. If there is already a .Rmd file with the same name in the output directory, the function will raise an error and stop, to avoid overwriting the existing file. The reason for this behaviour is that the copied template in the output directory will be deleted once the report is generated.

Generates a summary report in the outputDir directory, and returns (invisibly) the name of the generated report.

Charlotte Soneson

alevinQCReport(baseDir = system.file("extdata/alevin_example_v0.14",
                                     package = "alevinQC"),
               sampleId = "example", outputFile = "alevinReport.html",
               outputDir = tempdir(), forceOverwrite = TRUE)