Selects biomolecules for normalization via the method of rank-invariant biomolcules (RIP)
rip(e_data, edata_id, fdata_id, groupDF, alpha = 0.2)a \(p \times n\) 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.
character string indicating the name of the peptide, protein,
lipid, or metabolite identifier. Usually obtained by calling
attr(omicsData, "cnames")$edata_cname.
character string indicating the name of the sample column name in f_data.
data.frame created by group_designation with columns
for sample.id and group. If two main effects are provided the original main
effect levels for each sample are returned as the third and fourth columns
of the data.frame.
numeric p-value threshold, above which the biomolecules are retained as rank invariant (default value 0.25)
Character vector containing the biomolecules belonging to the RIP subset.
Biomolecules with complete data are subjected to a Kruskal-Wallis
test (non-parametric one-way ANOVA) on group membership, and those
biomolecules with p-value greater than a defined threshold alpha
(common values include 0.1 or 0.25) are retained as rank-invariant
biomolecules.