Function reference • ProFAST

All functions
`AddAdj()`	Calculate the adjacency matrix given a spatial coordinate matrix
`AddParSettingFAST()`	Add FAST model settings for a PRECASTObj object
`coembedding_umap()`	Calculate UMAP projections for coembedding of cells and features
`coembed_plot()`	Coembedding dimensional reduction plot
`CosMx_subset`	A Seurat object including spatial transcriptomics dataset from CosMx platform
`diagnostic.cor.eigs()`	Determine the dimension of low dimensional embedding
`FAST()`	Run FAST model for a PRECASTObj object
`FAST_run()`	(Varitional) ICM-EM algorithm for implementing FAST model
`FAST_single()`	Fit FAST model for single-section SRT data
`FAST_structure()`	(Varitional) ICM-EM algorithm for implementing FAST model with structurized parameters
`find.signature.genes()`	Find the signature genes for each group of cell/spots
`get.top.signature.dat()`	Obtain the top signature genes and related information
`get_r2_mcfadden()`	Calcuate the the adjusted McFadden's pseudo R-square
`IntegrateSRTData()`	Integrate multiple SRT data into a Seurat object
`iscmeb_run()`	Fit an iSC-MEB model using specified multi-section embeddings
`model_set_FAST()`	Set parameters for FAST model
`NCFM()`	Cell-feature coembedding for scRNA-seq data
`NCFM_fast()`	Cell-feature coembedding for SRT data
`pbmc3k_subset`	A Seurat object including scRNA-seq PBMC dataset
`pdistance()`	Calculate the cell-feature distance matrix
`RunHarmonyLouvain()`	Embedding alignment and clustering based on the embeddings from FAST
`RuniSCMEB()`	Fit an iSC-MEB model using the embeddings from FAST
`SelectHKgenes()`	Select housekeeping genes
`top5_signatures`	A data.frame object including top five signature genes in scRNA-seq PBMC dataset
`transferGeneNames()`	Transfer gene names from one fortmat to the other format

Reference

All functions