load_excel: Load metabolite data from an excel file

In XikunHan/metabolomicsR: Tools for Metabolomics Data

Load metabolite data from an excel file

Description

Load metabolite data from an excel file

Usage

load_excel(
  path,
  data_sheet = NULL,
  feature_sheet = NULL,
  sample_sheet = NULL,
  featureID = "CHEM_ID",
  sampleID = "PARENT_SAMPLE_NAME"
)

Arguments

path	Path to the xls/xlsx file.
data_sheet	A integer of xlsx sheet number for metabolite measurements (peak area data or normalized data, sample [row] * feature [column])
feature_sheet	A integer of xlsx sheet number for metabolite annotation (chemical annotation)
sample_sheet	A integer of xlsx sheet number for 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.

Examples

file_path <- system.file("extdata", "QMDiab_metabolomics_OrigScale.xlsx", 
package = "metabolomicsR", mustWork = TRUE)

df_plasma <- load_excel(path = file_path, data_sheet = 1, feature_sheet = 4, sample_sheet = 8, 
sampleID = "QMDiab-ID", featureID = "BIOCHEMICAL")

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