assessBusco: The function to classify the founded ortholog based on its...

In giangnguyen0709/fCAT: fCAT

Description

The function to classify the founded ortholog based on its length

Usage

assessBusco(orthoLength, root, coreSet, coreGene, f)

Arguments

orthoLength	the length of the ortholg sequence
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 gene
f	the appearance frequence of the core gene in the phylogenetic profile

Value

the status of the core gene, it can be "fragmented", "complete", "duplicated, complete" or "duplicated, fragmented"

Examples

coreFolder <- system.file("extdata", "sample", package = "fCAT")
status <- assessBusco(600, coreFolder, "test", "530670", f = 1)
print(status)

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