iscmeb_run: Fit an iSC-MEB model using specified multi-section embeddings
In ProFAST: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

iscmeb_run

R Documentation

Fit an iSC-MEB model using specified multi-section embeddings

Description

Integrate multiple SRT data based on the PRECASTObj by FAST and iSC-MEB model fitting.

Usage

iscmeb_run(
  VList,
  AdjList,
  K,
  beta_grid = seq(0, 5, by = 0.2),
  maxIter = 25,
  epsLogLik = 1e-05,
  verbose = TRUE,
  int.model = "EEE",
  init.start = 1,
  Sigma_equal = FALSE,
  Sigma_diag = TRUE,
  seed = 1
)

Arguments

`VList`	a M-length list of embeddings. The i-th element is a ni * q matrtix, where ni is the number of spots of sample i, and q is the number of embeddings. We provide this interface for those users who would like to define the embeddings by themselves.
`AdjList`	an M-length list of sparse matrices with class `dgCMatrix`, specify the adjacency matrix used for intrisic CAR model in FAST. We provide this interface for those users who would like to define the adjacency matrix by themselves.
`K`	an integer, specify the number of clusters.
`beta_grid`	an optional vector of positive value, the candidate set of the smoothing parameter to be searched by the grid-search optimization approach, defualt as a sequence starts from 0, ends with 5, increase by 0.2.
`maxIter`	the maximum iteration of ICM-EM algorithm. The default is 25.
`epsLogLik`	a string, the species, one of 'Human' and 'Mouse'.
`verbose`	an optional intger, spcify the number of housekeeping genes to be selected.
`int.model`	an optional string, specify which Gaussian mixture model is used in evaluting the initial values for iSC.MEB, default as "EEE"; and see `Mclust` for more models' names.
`init.start`	an optional number of times to calculate the initial value (1 by default). When init.start is larger than 1, initial value will be determined by log likelihood of mclust results.
`Sigma_equal`	an optional logical value, specify whether Sigmaks are equal, default as `FALSE`.
`Sigma_diag`	an optional logical value, specify whether Sigmaks are diagonal matrices, default as `TRUE`.
`seed`	an optional integer, the random seed in fitting iSC-MEB model.