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Processed metabolomics data used for differential analysis

Source: R/data.R
METAB_NORM_DATA_NESTED.Rd

Combined sample-level data organized by metabolomics platforms and tissue used for differential analysis

Usage

METAB_NORM_DATA_NESTED

Format

A nested list of data frames

Details

METAB sample-level data is in a different format than sample-level data for other assays/omes. Extract data from a panel and tissue using METAB_NORM_DATA_NESTED[[platform]][[tissue]], where platform is one of "metab-t-amines", "metab-t-acoa", "metab-t-nuc", "metab-t-oxylipneg", "metab-t-ka", "metab-t-etamidpos", "metab-t-tca", "metab-u-lrppos", "metab-u-lrpneg", "metab-u-hilicpos", "metab-u-rppos", "metab-u-rpneg", "metab-u-ionpneg" (see MotrpacBicQC::assay_codes for details) and tissue is a tissue abbreviation (see TISSUE_ABBREV). Samples (vial labels) are in columns, and metabolites (feature IDs) are in rows. Feature IDs in the row names in these tables correspond to METAB_FEATURE_ID_MAP$feature_ID_sample_data.

Not all data sets were processed similarly. The processing for each tissue/platform data follows this criteria:

  • Metabolomics targeted 't' platform with >12 features: KNN-imputed and log2-transformed

  • Metabolomics targeted 't' platform with <= 12 features: Log2-transformed (no imputation)

  • Metabolomics untargeted 'u' platform: sample-centered, KNN-imputed, log2-transformed