Run Quality Control Checks — run

This function takes a `gimap_dataset` and creates a QC report

run_qc(
  gimap_dataset,
  output_file = "./gimap_QC_Report.Rmd",
  plots_dir = "./qc_plots",
  overwrite = FALSE,
  filter_zerocount_target_col = NULL,
  filter_plasmid_target_col = NULL,
  filter_replicates_target_col = NULL,
  ...
)

Arguments

gimap_dataset: A special dataset structure that is setup using the `setup_data()` function.
output_file: default is `QC_Report`; name of the output QC report file
plots_dir: default is `./qc_plots`; 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
...: additional parameters are sent to `rmarkdown::render()`

Value

a QC report saved locally

Examples

if (FALSE) { # \dontrun{

gimap_dataset <- get_example_data("gimap")

run_qc(gimap_dataset)
} # }