load_data: Load metabolite data from three separate files

In XikunHan/metabolomicsR: Tools for Metabolomics Data

Load metabolite data from three separate files

Description

Load metabolite data from three separate files (import files using 'fread' from data.table).

Usage

load_data(
  data_path = NULL,
  feature_path = NULL,
  sample_path = NULL,
  featureID = "CHEM_ID",
  sampleID = "PARENT_SAMPLE_NAME"
)

Arguments

data_path	Path to the metabolite measurements (peak area data or normalized data, sample [row] * feature [column])
feature_path	Path to the metabolite annotation (chemical annotation)
sample_path	Path to the sample annotation (sample meta data)
featureID	a character of the metabolite ID column (in feature file and the column names of data file), default: CHEM_ID (provided from Metabolon file)
sampleID	a character of the sample ID column (in sample file and the first column of data file), default: PARENT_SAMPLE_NAME (provided from Metabolon file).

Value

A Metabolite object with slots: assayData, featureData, and sampleData.

XikunHan/metabolomicsR documentation built on Oct. 14, 2024, 3:18 p.m.