CountClust (version 1.0.2)

FitGoM: Grade of Membership (GoM) model fit !

Description

Fits a grade of membership model to count data. Default input includes a sample-by-feature matrix, the number of clusters (topics) to fit (K). The function is a wrapper of the topics() function implemented in Matt Taddy's maptpx pacakge.

Usage

FitGoM(data, K, tol, path_rda = NULL, control = list())

Arguments

data

counts data, with samples along the rows and features along the columns.

K

the vector of clusters or topics to be fitted.

tol

Tolerance value for GoM model log posterior increase at successive iterations (set to 0.1 as default).

path_rda

The directory path for saving the GoM model output. If NULL, it will return the output to console.

control

Control parameters. Same as topics() function of maptpx package.

Value

Saves the GoM model fit output for each cluster in vector K at the directory path in path_rda.

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=4, tol=1000, control=list(kill=1))