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

Source: R/PathwaybasedAnnotationStatistics.R
CalculateSingleAnnotationStatistics.Rd

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
)

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).

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

#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")