callGetLLBySample: Function callGetLLBySample
In CshlSiepelLab/ACE: Analysis of CRISPR Essentiality in R

Calls Rcpp functions to evaluate the likelihood of a single SAMPLE parameter given gene and guide parameters. Assumes sample independence.

If there is no initial sequencing, there is only lambda' (ModelObj$dep_scaling). If there is initial sequencing, there is also lambda (ModelObj$init_scaling). There is no scaling term for either form of the nsg prior (uniform or masterlibrary based); numerical evaluation is presumed to adjust lambda to re-scale nsg to counts, assuming a linear relationship between observed counts and the estimated prior as described by lambda.

callGetLLBySample(
  sample_effect,
  gene_effects,
  use_genes = NA,
  use_sample,
  guide_efficiency,
  user_DataObj,
  user_ModelObj
)

`sample_effect`	Tuple sample effect parameter.
`gene_effects`	Numeric vector of gene essentiality parameters.
`use_genes`	Subset of gene names to use (optional).
`use_sample`	Sample index corresponding to sample_effect.
`guide_efficiency`	Numeric vector of guide efficiency weights.
`user_DataObj`	DataObject with experimental data to analyze.
`user_ModelObj`	ModelObject with preprocessed model parameters.