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Create a Pathway Assay from Gene or Metabolite Data

Source: R/PathwayAnalysis.R
CreatePathwayAssay.Rd

This function creates a new assay within the provided SpaMTP Seurat object which contains features (either genes or metabolites) labeled by their respective RAMP ID. This assay can be used for running feature set co-regulation analysis (based on GSCA; doi:10.1093/bioinformatics/btp502 ).

Usage

CreatePathwayAssay(
  SpaMTP,
  analyte_type = "metabolites",
  assay = "Spatial",
  slot = "counts",
  new_assay = "pathway",
  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 containing either spatial metabolic or transcriptomic data

analyte_type

Character string specifying the type of analytes to process.Must be either "genes" or "metabolites" (default = "metabolites").

assay

Character string specifying the name of the assay to use as source data (default = "Spatial").

slot

Character string specifying which slot in the assay to use as source data (default = "counts").

new_assay

Character string specifying the name of the new assay to create (default = "pathway").

annotation_score_threshold

Minimum indexed annotation score used to map m/z features to RaMP compounds (default = 0.05).

annotation_source

Metabolite annotation provenance. "current" requires the indexed, scored RaMP output; "auto" and "legacy" enable compatibility with older serialized SpaMTP objects.

verbose

Boolean logical value indicating whether to print verbose messages during execution. (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 a new assay added, containing respective gene/metabolite data formatted based on RAMP_db IDs.

Examples

utils::str(formals(CreatePathwayAssay))
#> Dotted pair list of 12
#>  $ SpaMTP                    : symbol 
#>  $ analyte_type              : chr "metabolites"
#>  $ assay                     : chr "Spatial"
#>  $ slot                      : chr "counts"
#>  $ new_assay                 : chr "pathway"
#>  $ 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
## Create a pathway assay from metabolite data
#spamtp_obj <- CreatePathwayAssay(spamtp_obj, analyte_type = "metabolites", assay = "SPM", new_assay = "pathway")

## Create a pathway assay from gene data with verbose output
#spamtp_obj <- CreatePathwayAssay(spamtp_obj, analyte_type = "genes", assay = "SPT", new_assay = "gene_pathway", verbose = TRUE)