getLL: Function getLL For experiments with master library, initial...
In CshlSiepelLab/ACE: Analysis of CRISPR Essentiality in R

Function getLL For experiments with master library, initial infection, AND depleted samples sequenced. Call get_nb and get_poiss within cpp code, returning a likelihood value to optimize.

getLL(
  gene_essentiality,
  guide_efficiency,
  sample_effects,
  init_counts,
  dep_counts,
  var_model,
  master_freq,
  masterlib_key,
  cells_infected,
  init_scaling,
  dep_scaling,
  nsg_vals,
  var_params,
  step_size
)

`gene_essentiality`	NumericVector (for flexibility) by-guide essentiality to test.
`guide_efficiency`	NumericVector by-guide efficiency.
`sample_effects`	NumericVector by-sample effects on gene_essentiality.
`init_counts`	NumericMatrix
`dep_counts`	NumericMatrix
`var_model`	int specifying which count mean~variation model to use.
`master_freq`	NumericMatrix; log fraction of cells infected by each guide; rows correspond to guides, columns to different masterlibraries.
`masterlib_key`	NumericVector of columns of master_freq to use per sample.
`cells_infected`	NumericVector number of cells infected per sample in experiment.
`init_scaling`	NumericVector of scaling factors to normalize total read depth of initial sample.
`dep_scaling`	NumericVector of scaling factors to normalize total read depth and LFC ratio shifts due to guide drop-out.
`nsg_vals`	Vector of percent of cells infected (unobserved, integrating over.)
`var_params`	List of mean~variance model parameters (fit in ModelObj).
`step_size`	Intervals of infected cells for discrete integral evaluation.