Function reference • OikScrambling

All functions
`OikScrambling-package`	The OikScrambling package
`addMetadataToGRanges()`	Add metadata to a GenomicRanges object
`calcOperons()`	Calculate operon ranges by distance and colinearity
`compDistClass()`	Transform pair name into distance class.
`compDistance()`	Transform pair name into distance name.
`compGenus()`	Transform pair name into genus name.
`isSynbrachial()`	Flag pairs that are on homologous chromosome arms
`isSyntenic()`	Flag pairs that are on homologous chromosomes
`loadAllAnnotations()`	Load all annotations
`loadAllGenomes()`	Load all genomes
`loadAllRepeats()`	Load all repeat annotations
`loadAllTranscriptsGR()`	Load all transcript information as GRanges
`load_one_to_ones()`	Load one-to-one orthogroups for a set of species
`loaddNdSTable()`	Load dNdS data from OikScrambling data
`nameSynbrachial()`	Reports syntenic chromosome arm name or NA
`nameSyntenic()`	Reports syntenic chromosome name or NA
`removeUnplacedContigs()`	Remove unplaced contigs
`scafs`	Scaffolding guides

Reference