This function takes a `gimap_dataset` and creates a QC report
run_qc(
gimap_dataset,
output_file,
plots_dir,
overwrite = FALSE,
filter_zerocount_target_col = NULL,
filter_plasmid_target_col = NULL,
filter_replicates_target_col = NULL,
open_results = TRUE,
...
)Arguments
- gimap_dataset
A special dataset structure that is setup using the `setup_data()` function.
- output_file
Needs to be a string that ends with ".Rmd" What the name of the output QC report file should be.
- plots_dir
directory to save plots created with this function, if it doesn't exist already it will be created
- overwrite
default is FALSE; whether to overwrite the QC Report file
- filter_zerocount_target_col
default is NULL; Which sample column(s) should be used to check for counts of 0? If NULL and not specified, downstream analysis will select all sample columns
- filter_plasmid_target_col
default is NULL; Which sample columns(s) should be used to look at log2 CPM expression for plasmid pgRNA constructs? If NULL and not specified, downstream analysis will select the first sample column only
- filter_replicates_target_col
default is NULL; Which sample columns are replicates whose variation you'd like to analyze; If NULL, the last 3 sample columns are used
- open_results
default is TRUE but if you don't want the report automatically opened, choose FALSE.
- ...
additional parameters are sent to `rmarkdown::render()`
Value
a QC report saved locally
Examples
gimap_dataset <- get_example_data("gimap")
run_qc(
gimap_dataset,
plots_dir = tempdir(),
output_file = paste0(tempfile(), "_QC_Report.Rmd")
)
#>
#>
#> processing file: fileaa27480407ae_QC_Report.Rmd
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#> 2/22 [setup]
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#> 4/22 [unnamed-chunk-1]
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#> 18/22 [unnamed-chunk-8]
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#> 22/22 [unnamed-chunk-10]
#> output file: fileaa27480407ae_QC_Report.knit.md
#> /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/x86_64/pandoc +RTS -K512m -RTS fileaa27480407ae_QC_Report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output fileaa27480407ae_QC_Report.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 3 --variable toc_float=1 --variable toc_selectors=h1,h2,h3 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=spacelab --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/2d/d8927cd105550jjcy7qy99_w0000gn/T//RtmpIhnhWL/rmarkdown-straa2775912e82.html --variable code_folding=show --variable code_menu=1
#>
#> Output created: fileaa27480407ae_QC_Report.html
#> Results in: /var/folders/2d/d8927cd105550jjcy7qy99_w0000gn/T//RtmpIhnhWL/fileaa27480407ae_QC_Report.html
#> [1] "/var/folders/2d/d8927cd105550jjcy7qy99_w0000gn/T//RtmpIhnhWL/fileaa27480407ae_QC_Report.html"