Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

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Documentation for package ‘ProFAST’ version 1.4

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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
diagnostic.cor.eigs.default Determine the dimension of low dimensional embedding
diagnostic.cor.eigs.Seurat 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