Table 3 Common generic methods defined in patRoon to process workflow data

length(), show(), algorithm(), names(), groupNames()

Obtain general object information such as object length and unique identifiers for contained results

filter()

Rule-based filtering operations

[, [[, $ operators

Subsetting or extracting data

as.data.table(), as.data.frame()

Conversion to data.table or data.frame object

unique(), overlap()

Extract unique or overlapping features across replicates

consensus()

Generates a consensus between different objects of the same class

plot(), plotEIC(),

plotSpec()

Plot general, chromatographic and annotation data

plotChord(), plotUpSet(), plotVenn()

Comparison of feature data or workflow objects from different algorithms by chord, UpSet and Venn diagrams