computeOriginal: The function compute the initial original phylogenetic...
In giangnguyen0709/fCAT: fCAT

The function compute the initial original phylogenetic profile of all the taxa in the score set

computeOriginal(
    coreDir, coreSet, scoreMode, cpu = 4, cleanup = FALSE,
    ppDir = NULL
)

`coreDir`	The path to the core directory, where the core set is stored within weight_dir, blast_dir, etc.
`coreSet`	The name of the interested core set. The core directory can contains more than one core set and the user must specify the interested core set. The core set will be stored in the folder core_orthologs in subfolder, specify them by the name of the subfolder
`scoreMode`	the mode determines the method to scoring the founded ortholog and how to classify them. Choices: 1, 2, 3, "busco"
`cpu`	determines the cores that fDOG and fdogFAS will uses to be run parallel
`cleanup`	The fDOG's output is a set of phylogenetic profile of each core group to the interested genome. The phylogenetic profile will be stored into a folder in the core set. The function will merge all the small phylogenetic profile, calculate the FAS score or length to have the whole phylogenetic profile of the interested genome to the core set. This fDOG's output can be reused for all score modes. When cleanup is set to TRUE, the fDOG's output will not be stored to be reused but to be removed
`ppDir`	The user can replace the default folder output in the core directory, where the phylogenetic profiles are stored by his folder. The user can specify the path to his folder in this argument