Chapter 2 Data Import

The first key step in using Venndir is to import data in a recognized format. There are several formats available:

  • List of sets, referred to as a setlist
    • a list of character item vectors.
    • sets are represented by names(setlist)
  • List of signed sets, referred to as a signed setlist
    • a list of signed numeric vectors.
    • signed vectors use values -1 or 1, and store items in names().
    • sets are represented by names(setlist)
  • Incidence matrix
    • a numeric matrix with items as rownames(), sets as colnames().
    • items are indicated by the value 1 in the appropriate row and column.
  • Signed incidence matrix
    • a numeric matrix with items as rownames(), sets as colnames().
    • items are indicated by -1 or 1 in the appropriate row and column.
  • Overlap counts
    • a numeric vector with the number of items in each overlap.
    • the overlap name is stored in names(), in format: 'A', 'B', 'A&B'.
  • Signed overlap counts
    • a list of numeric vectors, named by overlap set.
    • each overlap is also a list named by the directionality.
  • Other formats
  • Specialized formats