fit_gaussians: Fit a mixture of Gaussians to a chromatogram curve

In fosterlab/PrInCE: Predicting Interactomes from Co-Elution

Description

Fit mixtures of one or more Gaussians to the curve formed by a chromatogram profile, using nonlinear least-squares.

Usage

fit_gaussians(
  chromatogram,
  n_gaussians,
  max_iterations = 10,
  min_R_squared = 0.5,
  method = c("guess", "random"),
  filter_gaussians_center = TRUE,
  filter_gaussians_height = 0.15,
  filter_gaussians_variance_min = 0.1,
  filter_gaussians_variance_max = 50
)

Arguments

chromatogram	a numeric vector corresponding to the chromatogram trace
n_gaussians	the number of Gaussians to fit
max_iterations	the number of times to try fitting the curve with different initial conditions; defaults to 10
min_R_squared	the minimum R-squared value to accept when fitting the curve with different initial conditions; defaults to 0.5
method	the method used to select the initial conditions for nonlinear least squares optimization (one of "guess" or "random"); see make_initial_conditions for details
filter_gaussians_center	true or false: filter Gaussians whose centres fall outside the bounds of the chromatogram
filter_gaussians_height	Gaussians whose heights are below this fraction of the chromatogram height will be filtered. Setting this value to zero disables height-based filtering of fit Gaussians
filter_gaussians_variance_min	Gaussians whose variance falls below this number of fractions will be filtered. Setting this value to zero disables filtering.
filter_gaussians_variance_max	Gaussians whose variance is above this number of fractions will be filtered. Setting this value to zero disables filtering.

Value

a list with six entries: the number of Gaussians used to fit the curve; the R^2 of the fit; the number of iterations used to fit the curve with different initial conditions; the coefficients of the fit model; and the fit curve predicted by the fit model.

Examples

data(scott)
chrom <- clean_profile(scott[1, ])
fit <- fit_gaussians(chrom, n_gaussians = 1)

fosterlab/PrInCE documentation built on Dec. 13, 2020, 5:50 a.m.