In bihealth/metaquac: Metabolomics Targeted Quality Control

Data export

The fully preprocessed dataset 4 is exported for further analysis in R, Excel, etc. This means the export provides a fully merged dataset with respect to injection pairs as well as potentially different batches, which compounds and samples were filtered as described in the preprocessing section.

To access data from intermediary preprocessing steps, please refer to the corresponding tables in the preprocessing section.

export_prefix <- file.path(params$export_dir, params$export_name)
export_dataset <- datasets$filter_samples_by_compound_mv_kept
save(export_dataset, file = paste0(export_prefix, ".RData"))
readr::write_csv(export_dataset, paste0(export_prefix, ".csv"))
readr::write_tsv(export_dataset, paste0(export_prefix, ".tsv"))

Exported preprocessed/filtered Biocrates data as:

• RData: r paste0(export_prefix, ".RData")
• Csv: r paste0(export_prefix, ".csv")
• Tsv: r paste0(export_prefix, ".tsv")

bihealth/metaquac documentation built on Aug. 7, 2021, 8:40 a.m.