This the function used to compute the gene/metabolites set enrichment for multi-omics spatial data
Usage
FindRegionalPathways(
SpaMTP,
ident,
DE.list,
analyte_types = c("genes", "metabolites"),
SM_assay = "SPM",
ST_assay = "SPT",
SM_slot = "counts",
ST_slot = "counts",
min_path_size = 5,
max_path_size = 500,
pval_cutoff_mets = 0.05,
pval_cutoff_genes = 0.05,
verbose = TRUE
)Arguments
- SpaMTP
A SpaMTP Seurat object contains spatial metabolomics(SM)/transcriptomics(ST) data or both, if contains SM data, it should be annotated via SpaMTP::AnnotateSM function.
- ident
A name character to specific the cluster vector for regions in
SpaMTP@meta.dataslot.- DE.list
A list consisting of differential expression data.frames for each input modality. Within each data.frame column names MUST include 'cluster', 'gene', ('avg_log2FC' or 'logFC') and ('p_val_adj' or 'FDR').
- analyte_types
Vector of character strings defining which analyte types to use. Options can be c("genes"), c("metabolites") or both (default = c("genes", "metabolites")).
- SM_assay
A Character string defining describing slot name for spatial metabolomics data in SpaMTP to extract intensity values from (default = "SPM").
- ST_assay
A Character string defining describing slot name for spatial transcriptomics data in SpaMTP to extract RNA count values from (default = "SPT").
- SM_slot
The slot name containing the SM assay matrix data (default = "counts").
- ST_slot
The slot name containing the ST assay matrix data (default = "counts").
- min_path_size
The min number of metabolites in a specific pathway (default = 5).
- max_path_size
The max number of metabolites in a specific pathway (default = 500).
- pval_cutoff_mets
A numerical value defining the adjusted p value cutoff for significant differentially expressed metabolites. If
NULLcutoff =0.05(default = 0.05).- pval_cutoff_genes
A numerical value defining the adjusted p value cutoff for significant differentially expressed genes. If
NULLcutoff =0.05(default = 0.05).- verbose
Boolean indicating whether to show informative messages. If FALSE these messages will be suppressed (default = TRUE).