# Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

## Documentation for package ‘ProFAST’ version 1.9

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## Help Pages

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