ppp {pmartR}

Identify Biomolecules from the Proportion Present (PPP) for Use in Normalization

Description

Selects biomolecules for normalization via the method of percentage of the peptides (or proteins, metabolites, etc.) present (PPP)

Usage

ppp(e_data, edata_id, proportion = 0.5)

Arguments

e_data

a p \times n + 1 data.frame, where p is the number of peptides, proteins, lipids, or metabolites and n is the number of samples. Each row corresponds to data for a peptide, protein, lipid, or metabolite, with one column giving the biomolecule identifier name.

edata_id

character string indicating the name of the peptide, protein, lipid, or metabolite identifier. Usually obtained by calling attr(omicsData, "cnames")$edata_cname.

proportion

numeric value between 0 and 1, indicating the proportion at or above which a biomolecule must be present across all samples in order to be retained (default value 0.5)

Details

Biomolecules present across proportion samples are designated as PPP.

Value

Character vector containing the biomolecules belonging to the PPP subset.

Author(s)

Kelly Stratton