cutfind2: @title Cutfind @description finds summary stats for...

In JulianSpagnuolo/FACkit: FACS Analysis Tool Kit

Description

@param x data.frame or named matrix containing raw data for which you wish to identify cutoff values for subsequent transformation. @param markers a vector containing the columns in x that you wish to parse through cutfind2 @param npeaks a named vector of integers indicating the number of peaks in each distribution that you wish to identify. This can contain NA values. See details @param DensityThreshold Named numeric vector indicating the density above which peaks will be identified. Set this below the smallest peak in the density distribution of your data. @param gridsize gridsize used in the density estimation steps - this needn't be changed. @param epsilon accuracy of mixture modelling step (only used if npeaks for marker is > 1) @param maxit maximum iterations used by mixture modelling step (only used if npeaks for marker is > 1). If this step fails, it will restart (number of restarts set by max.restarts) and add 2000 iterations to maxit. @param max.restarts maximum restarts allowed in the mixture modelling steps (increases maxit by 2000 each restart). The function will use the parameters returned by the mixture modelling step to re-seed the algorithm. @param seed This is the system seed used by the mixture modelling step, just to increase the reproducibility of the function @param auto Logical - if TRUE the function will search for the optimal number of components (distributions) to fit in the mixture model by searching a range of +/- 2 peaks from the number of peaks identified. @param metric vector - the metric used to choose the optimum mixture model to fit to the data choose one of "BIC", "AIC", or "ICL" @param which.dev integer - the number of deviations from the peak at which to set the cutoff value. Default = 2 @details

Usage

cutfind2(x, markers, npeaks = NULL, DensityThreshold = NULL,
  gridsize = 14000, max.restarts = 1, epsilon = 1e-09,
  maxit = 8000, seed = 42, auto = TRUE, metric = "AIC",
  which.dev = 2)

JulianSpagnuolo/FACkit documentation built on June 24, 2019, 12:18 p.m.