run_qc: Run Quality Control Checks

In gimap: Calculate Genetic Interactions for Paired CRISPR Targets

Run Quality Control Checks

Description

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

Usage

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

## Not run: 

gimap_dataset <- get_example_data("gimap")

run_qc(
  gimap_dataset,
  plots_dir = tempdir(),
  output_file = paste0(tempfile(), "_QC_Report.Rmd")
)

## End(Not run)

gimap documentation built on June 8, 2025, 10:13 a.m.