Calculate annotation statistics for a single m/z value suggesting the most likely metabolite based on correlated pathway expression. — CalculateSingleAnnotationStatistics • SpaMTP

This function evaluates the potential biological relevance of an annotation for a given m/z value by:

Identifying pathways associated with each possible annotated metabolite
Calculating colocalisation score between the m/z intensity and the expression of each corresponding pathway
Ranking annotations by a combined z-score based on correlation strength and number of supporting significant pathways
NOTE: this function requires CreatePathwayAssay and CreatePathwayObject to be run first

Usage

CalculateSingleAnnotationStatistics(
  mz,
  data,
  mz.assay,
  pathway.assay = "pathway",
  mz.slot = "scale.data",
  pathway.slot = "scale.data",
  corr_theshold = 0,
  corr_weight = 1,
  n_weight = 1,
  database = NULL,
  database_version = "latest",
  database_source = c("auto", "bundled", "local"),
  database_local_dir = NULL
)

Arguments

mz: Character or numeric. The target m/z feature. If numeric, the closest matching m/z in the dataset will be selected.
data: A SpaMTP Seurat object containing both metabolite and pathway assays generated from CreatePathwayObject.
mz.assay: Character string defining the name of the assay containing m/z features.
pathway.assay: Character string matching the name of the assay containing pathway features (default = "pathway").
mz.slot: Character string stating the slot to extract m/z values from (default = "scale.data").
pathway.slot: Character string defining the slot to extract pathway features from (default = "scale.data").
corr_theshold: Numeric value stating the correlation threshold to consider a pathway as significantly colocalized. If set to 0, all pathways will be counted (default = 0).
corr_weight: Numeric weight applied to correlation score in z-score calculation. If significance should be based more on the correlation, increase this value (default = 1).
n_weight: Numeric weight applied to number of correlated pathways in z-score calculation (default = 1).
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 tibble with the ranked annotations for the m/z value, containing:

metabolite: Most common name of the metabolite associated with the RAMP ID
ramp_id: The RAMP ID corresponding to the annotation
n_sig_path: Number of correlated pathways above the threshold
max_cor: Maximum correlation value among significant pathways
z_score: Combined z-score used to rank annotations
pval: Unadjusted p-value
pval_adj: Adjusted p-value (BH method)

Examples

utils::str(formals(CalculateSingleAnnotationStatistics))
#> Dotted pair list of 13
#>  $ mz                : symbol 
#>  $ data              : symbol 
#>  $ mz.assay          : symbol 
#>  $ pathway.assay     : chr "pathway"
#>  $ mz.slot           : chr "scale.data"
#>  $ pathway.slot      : chr "scale.data"
#>  $ corr_theshold     : num 0
#>  $ corr_weight       : num 1
#>  $ n_weight          : num 1
#>  $ database          : NULL
#>  $ database_version  : chr "latest"
#>  $ database_source   : language c("auto", "bundled", "local")
#>  $ database_local_dir: NULL
#data <- CreatePathwayObject(data,assay="SPT_pathway",slot = "scale.data")
#CalculateSingleAnnotationStatistics(mz = "mz-674.2805",data = data,mz.assay = "SPM",pathway.assay = "pathway",mz.slot = "scale.data")