getLfcDt: getLfcDt: Function to retrieve average log fold change of...
In CshlSiepelLab/ACE: Analysis of CRISPR Essentiality in R

Takes geometric average across all guides and samples applying to a gene. If negative controls provided, normalizes final averages to mean of negative controls. Adds a pseudocount of 0.5 to the count data after scaling all counts to 1e7 reads per sample. Returns log2 of dep/init ratio.

getLfcDt(
  user_DataObj,
  isSim,
  use_base_counts = NA,
  use_samples = NA,
  getCI = T,
  lfcFileName = "lfc",
  writeFile = F,
  subset_base = T,
  write_log,
  neg_ctrl_file = NA
)

`user_DataObj`	DataObj to analyze.
`isSim`	Boolean whether data counts simulated; if so, true phi in name.
`use_base_counts`	Depleted-count-matched data.table to use as the denominator for fold change.
`use_samples`	Default NA, return results for only a sample subset.
`getCI`	Default true, return confidence intervals per phi. Sim only.
`lfcFileName`	Optional name of output file of lfc values.
`writeFile`	Boolean default false; should output file be written.
`subset_base`	Boolean default true; should use_base_counts be subset by use_samples?
`write_log`	Function to output log file.
`neg_ctrl_file`	Name of file containing gene names to use as negative controls. Optional; default is file used by user_DataObj.