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Regional Pathway Enrichment

Source: R/PathwayAnalysis.R
FindRegionalPathways.Rd

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,
  annotation_score_threshold = 0.05,
  annotation_source = c("current", "auto", "legacy"),
  verbose = TRUE,
  database = NULL,
  database_version = "latest",
  database_source = c("auto", "bundled", "local"),
  database_local_dir = NULL
)

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.data slot.

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

Adjusted p-value cutoff used when constructing metabolite ranks. Set to 1 to include annotated metabolites regardless of DE significance (default = 0.05).

pval_cutoff_genes

A numerical value defining the adjusted p value cutoff for significant differentially expressed genes. If NULL cutoff = 0.05 (default = 0.05).

annotation_score_threshold

Minimum indexed annotation score used for pathway mapping. It can be changed without re-running AnnotateSM() when the object was annotated with min_score = 0 (default = 0.05).

annotation_source

Metabolite annotation provenance. The default, "current", requires scored RaMP IDs from the indexed annotation pipeline. "auto" permits a warned fallback to legacy @tools$db_3, while "legacy" explicitly requests that compatibility path.

verbose

Boolean indicating whether to show informative messages. If FALSE these messages will be suppressed (default = TRUE).

database

Optional named list of database resources, normally created by LoadSpaMTPDatabase().

database_version

Database snapshot version used for pathway lookup.

database_source

Database source; see LoadSpaMTPDatabase().

database_local_dir

Optional local RDS resource directory.

Value

A SpaMTP object with set enrichment on given analyte types.

Examples

utils::str(formals(FindRegionalPathways))
#> Dotted pair list of 19
#>  $ SpaMTP                    : symbol 
#>  $ ident                     : symbol 
#>  $ DE.list                   : symbol 
#>  $ analyte_types             : language c("genes", "metabolites")
#>  $ SM_assay                  : chr "SPM"
#>  $ ST_assay                  : chr "SPT"
#>  $ SM_slot                   : chr "counts"
#>  $ ST_slot                   : chr "counts"
#>  $ min_path_size             : num 5
#>  $ max_path_size             : num 500
#>  $ pval_cutoff_mets          : num 0.05
#>  $ pval_cutoff_genes         : num 0.05
#>  $ annotation_score_threshold: num 0.05
#>  $ annotation_source         : language c("current", "auto", "legacy")
#>  $ verbose                   : logi TRUE
#>  $ database                  : NULL
#>  $ database_version          : chr "latest"
#>  $ database_source           : language c("auto", "bundled", "local")
#>  $ database_local_dir        : NULL
# SpaMTP = FindRegionalPathways(SpaMTP, polarity = "positive")