assessStatus: The function to classify a founded ortholog from its...
In giangnguyen0709/fCAT: fCAT

The function to classify a founded ortholog from its information like FAS scores, the appearance frequence of the core gene in phylogenetic profile, etc.

1	assessStatus(fasF, fasB, root, coreSet, coreGene, scoreMode, f, priorityList)

`fasF`	the forward fas score of the ortholog
`fasB`	the backward fas score of the ortholog
`root`	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
`coreGene`	the ID of the core group
`scoreMode`	the mode determines the method to scoring the founded ortholog and how to classify them. Choices: 1, 2, 3, "busco"
`f`	the appearance frequence of the core gene in the phylogenetic profile
`priorityList`	A list contains one or many genome ID of the genomes, which were used to build the core set. The genome ID of this list will be stored with an priority order, the tool look at into the fasta file of each core group and determine with the priority order to determine the references species for each core group.

the status of the ortholog of the core gene. It can be "similar", "dissimilar", "duplicated, similar" or "duplicated, dissimilar" #' @examples coreFolder <- system.file("extdata", "sample", package = "fCAT") status <- assessStatus( 0.7, 0.9, coreFolder, "test", "530670", scoreMode = 2, f = 1, priorityList = c("HUMAN@9606@1")) print(status)

giangnguyen0709/fCAT documentation built on Feb. 10, 2021, 4:31 a.m.