Identify Reference Site

Source: R/calibration_functions.R

Sites are ranked according to mean-squared error calculated between site-specific parameters and overall median parameter values (pooled across all timePoints and sites), and top ranking site is returned.

identifyReference(
  object,
  which.assay = NULL,
  which.parameter = NULL,
  which.phantom = NULL,
  which.data = "uncalibrated",
  pool.phantoms = F,
  return.scores = F
)

Arguments

object

Calibration Object
which.assay

Character specifying which assay to identify reference site for.
which.parameter

Character specifying which parameters to consider when selecting reference site
which.phantom

Character specifying which phantoms to select reference sites for. If unspecified, all phantoms are considered.
which.data

Character specifying which data to identify reference site for.
pool.phantoms

Logical specifying whether to pool ranking scores across all phantoms (true), or to rank phantoms separately (false, default).
return.scores

Logical indicating whether list of scores are returned. If false (default), reference sites are returned only.

Value

If return.scores is false, named vector of character(s) specfying reference site is returned. In case of tie, multiple sites are returned. If return.scores is true, list of site rankings is returned.

See also

consistencyAnalysis, consistencyPlot