MTBLS404_meta_data: Sampple meta data of 'Sacurine' data set from MetaboLights...

In computational-metabolomics/structData: Metabolomics data sets to demonstrate functionality of the qcrms package

Description

Sample meta data from Metabolights repositotry of the MTBLS404 project. Resulting xlsx file was generated using code below.

library(openxlsx)
library(dplyr)

mzml_files <- dir(system.file("extdata/MTBLS404/mzML", package="structData"),
    full.names=TRUE, recursive=TRUE)

mzml_filenames <- mzml_files <- dir(system.file("extdata/MTBLS404/mzML",
    package="structData"), full.names=FALSE, recursive=TRUE)

download.file(destfile = "s_sacurine.txt", mode="wb",
url = "https://www.ebi.ac.uk/metabolights/ws/studies/MTBLS404/download/
    dc11f678-8ae1-423f-a075-5403ef2638e7?file=s_sacurine.txt")

raw_sample_meta_data <- read.csv("s_sacurine.txt", sep="\t")

raw_sample_meta_data <-
raw_sample_meta_data[, c("Sample.Name", "Factor.Value.Age.",
    "Factor.Value.BMI.", "Factor.Value.Gender.", "Factor.Value.Osmolality.")]

sample_meta_data <- data.frame(File.Name=mzml_filenames)
sample_meta_data$Sample <- sub("\.mzML", "", mzml_filenames)
sample_meta_data$Sample.Class <- "Sample"
sample_meta_data$Sample.Class[grep("Blanc", mzml_filenames)] <- "Blank"
sample_meta_data$Sample.Class[grep("QC", mzml_filenames)] <- "QC"
sample_meta_data$Batch <- 1
sample_meta_data$Batch[grep("_b2", mzml_filenames)] <- 2
sample_meta_data$Sample.Name <- sub("_neg", "", sample_meta_data$Sample)
sample_meta_data$Sample.Name <- sub("_b2", "", sample_meta_data$Sample.Name)

sample_meta_data <- dplyr::left_join(sample_meta_data, raw_sample_meta_data,
    by="Sample.Name")
sample_meta_data$Sample.Name <- NULL

wb <- openxlsx::createWorkbook()
openxlsx::addWorksheet(wb, "meta")
openxlsx::writeData(wb, "meta", sample_meta_data, rowNames=FALSE)
openxlsx::saveWorkbook(wb, "MTBLS404_meta_data.xlsx", overwrite=TRUE)

file.remove("s_sacurine.txt")

Value

Microsofot Excel xlsx file.

Source

https://www.ebi.ac.uk/metabolights/MTBLS404

References

Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C. 2012. Annotation of the Human Adult Urinary Metabolome and Metabolite Identification Using Ultra High Performance Liquid Chromatography Coupled to a Linear Quadrupole Ion Trap-Orbitrap Mass Spectrometer. Anal Chem. Aug 7;84(15):6429-37. doi: 10.1021/ac300829f.

Examples

library(openxlsx)
meta_data <- openxlsx::readWorkbook(
    system.file("extdata/MTBLS404/MTBLS404_meta_data.xlsx",
    package="structData")
)
head(meta_data)

computational-metabolomics/structData documentation built on June 11, 2020, 12:16 a.m.