specmine (version 2.0.3)

MAIT_identify_metabolites: MAIT metabolite identification

Description

Performs metabolite identification using MAIT.

Usage

MAIT_identify_metabolites(dataset, metadata.variable, 
xSet = NULL, data.folder = NULL, features = NULL, 
mass.tolerance = 0.5)

Arguments

dataset

list representing the dataset from a metabolomics experiment.

metadata.variable

metadata's variable.

xSet

xcmsSet object that can be passed.

data.folder

string indicating the data folder.

features

features that can be used to help to identify the metabolites.

mass.tolerance

mass tolerance.

Value

Returns an object resulted from identifyMetabolites function from MAIT package.

References

http://www.bioconductor.org/packages/release/bioc/html/MAIT.html

Examples

# NOT RUN {
  ## Example of MAIT metabolite identification
  data(spinalCord)
  library(MAIT)
  mait.metabolites = MAIT_identify_metabolites(spinalCord, "type", 
			features = "all", data.folder = "data",
			xSet = spinalCord$xSet)
  mait.metab.table = mait.metabolites@FeatureInfo@metaboliteTable
  mait.metab.table[which(mait.metab.table$Name != "Unknown"), 
  c(1,3,6)]
# }