FitGoM {CountClust} | R Documentation

## Run Grade of Membership (GoM) model with multiple starting points !

### Description

Fits grade of membership model `FitGoM()` to count data with multiple starting points and choose the best fit using BIC (Bayesian Information Criterion). the multiple starting points ensure that the output is more reliable.

### Usage

    FitGoM(data, K, tol = 0.1, num_trials = 1, options, path_rda = NULL,
      control = list())

### Arguments

`data` | counts data N x G, with N, the number of samples along the rows and G, number of genes along columns.
`K` | the vector of clusters or topics to be fitted. Must be an integer, unlike in ]`FitGom()`. So you need to apply this function separately for each K.
`tol` | Tolerance value for GoM model absolute log posterior increase at successive iterations (set to 0.1 as default).
`num_trials` | The number of trials with different starting points used.
`options` | the measure used to choose best fit, either "BF" or "BIC" measures can be used. BF is more trustworthy, but BIC can be used for better model comparison.
`path_rda` | The directory path for saving the GoM model output. If NULL, it will return the output to console.
`control` | Control parameters for the GoM model fits. Same as topics() function of maptpx package.

### Value

Outputs the best GoM model fit output for cluster K and saves it at the directory path in path_rda if the latter is provided.

### References

Matt Taddy. On Estimation and Selection for Topic Models. AISTATS 2012, JMLR W\&CP 22.

Pritchard, Jonathan K., Matthew Stephens, and Peter Donnelly. Inference of population structure using multilocus genotype data. Genetics 155.2 (2000): 945-959.

### Examples

    data("ex.counts")
    out <- FitGoM(ex.counts, K=2, tol=100, num_trials=5,
                       control=list(tmax=100))

[Package CountClust version 1.12.0 Index]