Differential analysis of merged metabolomics datasets — METAB

Timewise summary statistics and training FDR from differential analysis (DA) that tests the effect of training on each metabolite within each sex. One data frame per tissue.

Usage

METAB_PLASMA_DA

METAB_HIPPOC_DA

METAB_CORTEX_DA

METAB_HYPOTH_DA

METAB_SKMGN_DA

METAB_SKMVL_DA

METAB_HEART_DA

METAB_KIDNEY_DA

METAB_ADRNL_DA

METAB_COLON_DA

METAB_SPLEEN_DA

METAB_TESTES_DA

METAB_OVARY_DA

METAB_VENACV_DA

METAB_LUNG_DA

METAB_SMLINT_DA

METAB_LIVER_DA

METAB_BAT_DA

METAB_WATSC_DA

Format

A data frame with 27 variables:

feature: character, unique feature identifier in the format 'ASSAY_ABBREV;TISSUE_ABBREV;feature_ID' only for training-regulated features at 5% IHW FDR. For redundant differential features, 'feature_ID' is prepended with the specific platform to make unique identifiers. See REPEATED_FEATURES for details.
assay: character, assay abbreviation, one of ASSAY_ABBREV
assay_code: character, assay code used in data release. See MotrpacBicQC::assay_codes.
tissue: character, tissue abbreviation, one of TISSUE_ABBREV
tissue_code: character, tissue code used in data release. See MotrpacBicQC::bic_animal_tissue_code.
feature_ID: character, MoTrPAC feature identifier
dataset: character, metabolomics platform (metab-u-ionpneg, metab-u-lrpneg, metab-u-lrppos, metab-u-hilicpos, metab-u-rpneg, metab-u-rppos, metab-t-amines, metab-t-oxylipneg, metab-t-tca, metab-t-nuc, metab-t-acoa, metab-t-ka) the feature was measured in. 'meta-reg' specifies results from the metabolomics meta-regression for repeated features.
site: character, Chemical Analysis Site (CAS) name
is_targeted: logical, is this a targeted platform?
sex: character, one of 'male' or 'female'
comparison_group: character, time point of trained animals compared to the sex-matched sedentary control animals, one of '1w', '2w', '4w', '8w'
p_value: double, unadjusted p-value for the difference between 'comparison_group' and the group of sex-matched sedentary control animals
adj_p_value: double, adjusted p-value from 'p_value' column. P-values are BY-adjusted across all datasets within a given assay/ome.
logFC: double, log fold-change where the numerator is 'comparison_group', e.g., '1w', and the denominator is the group of sex-matched sedentary control animals
logFC_se: double, standard error of the log fold-change
tscore: double, t statistic
covariates: character, comma-separated list of adjustment variables or NA
comparison_average_intensity: double, average intensity among the replicates in 'comparison_group'
reference_average_intensity: double, average intensity among the replicates in the group of sex-matched sedentary control animals
metabolite_refmet: character, RefMet name of metabolite
cv: double, feature coefficient of variation in the dataset
metabolite: character, name of metabolite as appears in the CAS's data
control_cv: double, feature coefficient of variation in the dataset
mz: double, mass over charge
rt: double, retention time
neutral_mass: double, neutral mass
selection_fdr: double, adjusted training p-value used to select training-regulated analytes. P-values are IHW-adjusted across all datasets within a given assay with tissue as a covariate.

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Details

Reproduce our analysis with MotrpacRatTraining6mo::metab_training_da() and MotrpacRatTraining6mo::metab_timewise_da().