doHMRF_V2: doHMRF_V2

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

doHMRF_V2

Description

function to run HMRF model

Usage

doHMRF_V2(HMRF_init_obj, betas = c(0, 10, 5))

Arguments

HMRF_init_obj	return list of initHMRF() function
betas	a vector of three values: initial beta, beta increment, and number of betas

Details

This function will run a HMRF model after initialization of HMRF. Of note is the beta parameter, the smoothing parameter. We recommend running a range of betas, For example, betas=c(0,10,5) will run for the following betas: 0, 10, 20, 30, 40. betas=c(0,5,2) will run for betas: 0, 5, 10 Setting the beta can use the following guideline. If number of genes N is 10<N<50, set betas=c(0, 1, 20) If 50<N<100, set betas=c(0, 2, 25) If 100<N<500, set betas=c(0, 5, 20) Returns a list with class, probability, and model log-likelihood value.

Value

A list (see details)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.