gauss: Gaussian model components
In flowPloidy: Analyze flow cytometer data to determine sample ploidy

Description Arguments Details Value Author(s)

Components for modeling Gaussian features in flow histograms

`a1, a2, b1, b2, c1, c2`	area parameters
`Ma, Mb, Mc`	curve mean parameter
`Sa, Sb, Sc`	curve standard deviation parameter
`xx`	vector of histogram intensities
`linearity`	numeric, the ratio of G2/G1 peak means. When linearity is fixed, this is set to 2. Otherwise, it is fit as a model parameter bounded between flowPloidy:::linL and flowPloidy:::linH.

Typically the complete models will contain fA1 and fB1, which model the G1 peaks of the sample and the standard. In many cases, they will also contain fA2 and fB2, which model the G2 peaks. The G2 peaks are linked to the G1 peaks, in that they require some of the parameters from the G1 peaks as well (mean and standard deviation).

If the linearity parameter is set to "fixed", the G2 peaks will be fit as exactly 2 times the mean of the G1 peaks. If linearity is set to "variable", the ratio of the G2 peaks to the G1 peaks will be fit as a model parameter with an initial value of 2, and constrained to the range 1.5 – 2.5. (The range is coded as linL and linH. If in doubt, check the values of those, i.e., flowPloidy:::linL, flowPloidy:::linH, to be sure Tyler hasn't changed the range without updating this documentation!!)

Additionally, for each set of peaks (sample and standard(s)), a broadened rectangle component is included to model the S-phase. At present, this is component has a single parameter, the height of the rectangle. The standard deviation is fixed at 1. Allowing the SD to vary in the model fitting doesn't make an appreciable difference in my tests so far, so I've left it simple.

Tyler Smith

flowPloidy documentation built on Nov. 8, 2020, 8:04 p.m.