Integrate multiple SRT data based on the PRECASTObj by FAST and iSC-MEB model fitting.
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
)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.
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.
an integer, specify the number of clusters.
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.
the maximum iteration of ICM-EM algorithm. The default is 25.
a string, the species, one of 'Human' and 'Mouse'.
an optional intger, spcify the number of housekeeping genes to be selected.
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.
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.
an optional logical value, specify whether Sigmaks are equal, default as FALSE.
an optional logical value, specify whether Sigmaks are diagonal matrices, default as TRUE.
an optional integer, the random seed in fitting iSC-MEB model.
returns a iSCMEBResObj object which contains all model results.