QA functions for the MoTrPAC community

merge_phenotype_metabolomics

R Documentation

Merge phenotypic and metabolics results

Merge phenotypic data (phenotypes_pass1a06_short) and metabolomics merged results and metadata

merge_phenotype_metabolomics(df_long)

df_long

(data.frame) Long format of a metabolomics merged results

(data.frame) Merged file, including the following columns:

sample_id: Sample Id, including vial_label and site specific QC ids
sample_type: Metabolomics sample types. Check metabolomics data transfer guidelines
sample_order: Order of injection on Mass Spec
metabolite_name: Given name by every lab
refmet_name: Map of the metabolite name to the Metabolomics RefMet database
mz: mass over charge
rt: retention time
formula: chemical formula
neutral_mass: neutral mass
id: type of metabolite identification: "named", "unnamed"
metabolite: Merge "refmet" for "named" metabolites and "metabolite_name" for "unnamed" metabolites
quantification: Untargeted: Peak area, Targeted: absolute concentration (check "experimentalDetails" for unit)
tissue_code: MoTrPAC tissue code
tissue_name: Tissue name
group_time_point: Intervention group (Exercise / Control) + time point
sex: Animal Sex
site_code: Chemical Analysis Site (CAS) short abbreviation
group: Intervention group: Exercise / Control
condition: Sex + group + time-point
bioreplicate: Sex + group + time-point + sample_order