performanceEvaluation: Function to evaluate mWISE performance

In b2slab/mWISE: Untargeted LC-MS data annotation

Description

Function performanceEvaluation computes performance metrics when a reference table is available.

Usage

performanceEvaluation(
  Annotated.dataset,
  df.Ref,
  top.cmps,
  do.Par = TRUE,
  nClust
)

Arguments

Annotated.dataset	Object returned by mWISE.annotation function.
df.Ref	Reference data frame. It should contain a column named "Peak.Id" with a peak identifier that corresponds to the mWISE Peak identifier, and a column named "Kegg" with the reference KEGG identifiers.
top.cmps	Number of top compounds to be considered in performance evaluation.
do.Par	TRUE if parallel computing is required. Def: TRUE.
nClust	Number of clusters that may be used. Def: Number of clusters - 1.

Value

Function performanceEvaluation returns a data frame with the performance of each mWISE stage.

Examples

data("sample.keggDB")
Cpd.Add <- CpdaddPreparation(KeggDB = sample.keggDB, do.Par = FALSE)
data(sample.dataset)
Peak.List <- sample.dataset$Negative$Input
Intensity.idx <- seq(27,38)
data("sample.graph")
gMetab <- igraph::as.undirected(sample.graph)
Annotated.List <- mWISE.annotation(Peak.List = Peak.List,
                                   polarity = "negative",
                                   diffusion.input.type = "binary",
                                   score = "raw",
                                   Cpd.Add = Cpd.Add,
                                   graph = gMetab,
                                   Unique.Annotation = TRUE,
                                   Intensity.idx = Intensity.idx,
                                   do.Par = FALSE)
 df.Ref <- sample.dataset$Negative$Output
 performanceEvaluation(Annotated.dataset = Annotated.List, 
                       df.Ref = df.Ref, top.cmps = 3)

b2slab/mWISE documentation built on Feb. 2, 2022, 12:24 a.m.