QCprep function

QCprep

Helper function to pre-process the Nightingale Health metabolomics data-set before applying the MetaboAge score by van den Akker et al.

QCprep(mat, PARAM_metaboAge, quiet = TRUE, Nmax_zero = 1, Nmax_miss = 1)

Arguments

• mat: numeric data-frame NH-metabolomics matrix.
• PARAM_metaboAge: list containing all the parameters to compute the metaboAge (metabolic features list,BBMRI-nl means and SDs of the metabolic features, and coefficients)
• quiet: logical to suppress the messages in the console
• Nmax_zero: numberic value indicating the maximum number of zeros allowed per sample (Number suggested=1)
• Nmax_miss: numberic value indicating the maximum number of missing values allowed per sample (Number suggested=1)

Returns

Nightingale-metabolomics data-frame after pre-processing (checked for zeros, missing values, samples>5SD from the BBMRI-mean, imputing the missing values and z-scaled)

Examples

library(MiMIR)

#load the Nightignale metabolomics dataset
metabolic_measures <- synthetic_metabolic_dataset

#Pre-process the metabolic features
prepped_met<-QCprep(as.matrix(metabolic_measures[,metabolites_subsets$MET63]), PARAM_metaboAge)

References

This function is constructed to be able to follow the pre-processing steps described in: van den Akker Erik B. et al. (2020) Metabolic Age Based on the BBMRI-NL 1H-NMR Metabolomics Repository as Biomarker of Age-related Disease. Circulation: Genomic and Precision Medicine, 13, 541-547, doi:10.1161/CIRCULATIONAHA.114.013116

See Also

apply.fit