check_gaussians: Check the format of a list of Gaussians

In fosterlab/PrInCE-R: Predicting Interactomes from Co-Elution

Description

Test whether an input list of Gaussians conforms to the format expected by PrInCE: that is, a named list with five fields for each entry, i.e., the number of Gaussians in the mixture model, the r^2 value, the number of iterations used by nls, the coefficients of each model, and the fitted curve.

Usage

check_gaussians(
  gaussians,
  proteins = NULL,
  replicate_idx = NULL,
  n_error = 3,
  pct_warning = 0.1
)

Arguments

gaussians	the list of Gaussians
proteins	the complete set of input proteins
replicate_idx	the replicate being analyzed, if input proteins are provided; used to throw more informative error messages
n_error	minimum number of proteins that can have fitted Gaussians without throwing an error
pct_warning	minimum fraction of proteins that can have fitted Gaussians without giving a warning

Details

Optionally, some extra checks will be done on the fraction of proteins in the complete dataset for which a Gaussian mixture model could be fit, if provided. In particular, the function will throw an error if fewer than n_error proteins have a fitted Gaussian, and emit a warning if fewer than pct_warning do.

Value

TRUE if all conditions are met, but throws an error if any is not

Examples

data(scott_gaussians)
check_gaussians(scott_gaussians)

fosterlab/PrInCE-R documentation built on Dec. 11, 2020, 3:51 p.m.