nonlinearFitDist {MethylIT}  R Documentation 
A wrapper to call functions 'Weibull3P' and 'fitGGammaDist' to operate on list of GRanges.
nonlinearFitDist(LR, column = 9, dist.name = "Weibull", sample.size = 20, location.par = FALSE, absolute = FALSE, npoints = NULL, model = "all", maxiter = 1024, tol = 1e12, ftol = 1e12, ptol = 1e12, minFactor = 10^6, num.cores = NULL, tasks = 0L, maxfev = 1e+05, verbose = TRUE, ...)
LR 
A list of GRanges objects with information divergence values in their metacolumns. 
column 
An integer number denoting the index of the GRanges column where the information divergence is given. Default column = 1 
dist.name 
name of the distribution to fit: Weibull (default: "Weibull"), gamma with threeparameter (Gamma3P), gamma with twoparameter (Gamma2P), generalized gamma with threeparameter ("GGamma3P") or fourparameter ("GGamma4P"), and LogNormal (LogNorm). 
sample.size 
size of the sample 
location.par 
whether to consider the fitting to generalized gamma distribution (GGamma) including the location parameter, i.e., a GGamma with four parameters (GGamam4P). 
absolute 
Logic (default, FALSE). Total variation (TV, the difference of methylation levels) is normally an output in the downstream MethylIT analysis. If 'absolute = TRUE', then TV is transformed into TV, which is an information divergence that can be fitted to Weibull or to Generalized Gamma distribution. 
npoints 
number of points used in the fit 
model 
Optional. Only when dist.name = "Weibull". A selection of the distribution model, twoparameters and threeparameters Weibull model ("2P" and "3P"). Default is "all" and the model with the best AIC criterion is reported. Alternatively, just use dist.name = "Weibull2P" or dist.name = "Weibull3P". 
maxiter 
positive integer. Termination occurs when the number of iterations reaches maxiter. Default value: 1024 
tol 
A positive numeric value specifying the tolerance level for the relative offset convergence criterion. Default value: 1e12, 
ftol 
nonnegative numeric. Termination occurs when both the actual and predicted relative reductions in the sum of squares are at most ftol. Therefore, ftol measures the relative error desired in the sum of squares. Default value: 1e12 
ptol 
nonnegative numeric. Termination occurs when the relative error between two consecutive iterates is at most ptol. Therefore, ptol measures the relative error desired in the approximate solution. Default value: 1e12, 
minFactor 
A positive numeric value specifying the minimum stepsize factor allowed on any step in the iteration. The increment is calculated with a GaussNewton algorithm and successively halved until the residual sum of squares has been decreased or until the stepsize factor has been reduced below this limit. Default value: 10^6. 
num.cores 
The number of cores to use, i.e. at most how many child
processes will be run simultaneously (see

tasks 
integer(1). The number of tasks per job. value must be a scalar
integer >= 0L. In this documentation a job is defined as a single call to
a function, such as bplapply, bpmapply etc. A task is the division of the
X argument into chunks. When tasks == 0 (default), X is divided as evenly
as possible over the number of workers (see

maxfev 
integer; termination occurs when the number of calls to fn has reached maxfev. Note that nls.lm sets the value of maxfev to 100*(length(par) + 1) if maxfev = integer(), where par is the list or vector of parameters to be optimized. 
verbose 
If TRUE, prints the function log to stdout 
... 
other parameters 
The algorithm prepares the information divergence variable to try fitting Weibull or generalized gamma distribution model to the data. If Weibull distribution is selected (default: "Weibull"), function 'Weibull2P' first attempts fitting to the twoparameter Weibull CDF (Weibull2P). If Weibull2P did not fit, then the algorithm will try to fit Weibull3P. The LevenbergMarquardt algorithm implemented in R package 'minpack.lm' is used to perform the nonlinear fit. Crossvalidations for the nonlinear regressions (R.Cross.val) are performed in each methylome as described in reference [1]. In addition, Stein's formula for adjusted R squared (rho) is used as an estimator of the average crossvalidation predictive power [1].
If "GGamma3P" is selected the call to function 'fitGGammaDist' permits the fitting to the threeparameter GGamma CDF ("GGamma3P"). The fit to the fourparameter GGamma ("GGamma4P") is also available. GGamma distribution are fitted using a modification of LevenbergMarquardt algorithm implemented in function 'nls.lm' from the 'minpack.lm' R package. Notice that the fit to GGamma dsitribution is computationally time consuming (see ?fitGGammaDist for additional information).
Model table with coeficients and goodnessoffit results: Adj.R.Square, deviance, AIC, R.Cross.val, and rho, as well as, the coefficient covariance matrix.
Robersy Sanchez 01/31/2018 <https://github.com/genomaths>
R. Sanchez and S. A. Mackenzie, “Information Thermodynamics of Cytosine DNA Methylation,” PLoS One, vol. 11, no. 3, p. e0150427, Mar. 2016.
Stevens JP. Applied Multivariate Statistics for the Social Sciences. Fifth Edit. Routledge Academic; 2009.
gofReport
## Load a dataset with Hellinger Divergence of methylation levels on it. data(HD) ## The nonlinear fit based on threeparameter GGamma distribution nlms2 < nonlinearFitDist(HD, npoints = 100, dist.name = "GGamma3P", verbose = FALSE) ## Weilbull distribution is a particular case of GGamma. nlms < nonlinearFitDist(HD, npoints = 100, verbose = FALSE) ## The goodnessoffit indicators AIC suggests that the best fitted model is ## obtained with GGamma distribution (in this example). res < mapply(function(m1,m2) { as.numeric(c(Weibull = m1$AIC[1], GGamma = m2$AIC[1])) }, nlms, nlms2) rownames(res) <c("Weibull", "GGamma") res ## However, the Crossvalidations correlation coefficient is saying that ## the Weibull distribution would be a little better probability predictor. res < mapply(function(m1,m2) { as.numeric(c(Weibull = m1$R.Cross.val[1], GGamma = m2$R.Cross.val[1])) }, nlms, nlms2) rownames(res) <c("Weibull", "GGamma") res