Function to calculate the recovery rate from binary PPI assays.

Function to calculate the recovery rate from binary PPI assays.

recovery.rate(
  referenceSet = NULL,
  PPIdf = NULL,
  assay = "mean_cBRET",
  construct.scaling = NULL,
  range = c(0.25, 0.75),
  iter.scaler = TRUE,
  cutoff = "all",
  fns = "median",
  n.sd = 1,
  n.CI = 0.99,
  negative.reference = "RRS",
  complex.parameters = NULL,
  verbose = TRUE
)

Arguments

referenceSet:

reference PPI data set used to determine cutoffs to calculate recovery rates

PPIdf:

optional binary PPI data set containing interactions classified using the cutoffs from the reference sets

assay:

assay in the referenceSet and PPIdf to calculate recovery rates

construct.scaling:

scaling of constructs by "median.normalization" or "robust.scaler"

range:

probs in stats::quantile(x, ...): numeric vector of probabilities

iter.scaler:

if TRUE and when using "robust.scaler" it iteratively performs robust scaler normalization until the IQR of each construct is within the IQR of all loaded data sets

cutoff:

cutoffs are calculated based on "all" interactions, or for each "construct" or for each "orientation"

fns:

function used to calculate the cutoffs: "median", "mean", "CI" or "max"

n.sd:

number of sd used to calculate the cutoffs for functions "median" and "mean"

n.CI:

confidence intervall used to calculate the cutoff for function "CI"

negative.reference:

string in the column "complex" to specify the negative/random interactions

complex.parameters:

additional grouping parameters from which the recovery rates are calculated

verbose:

give detailed information

Value

a list with elements