filterIgnore: Determine if a core gene was ignored by the tool because of...

In giangnguyen0709/fCAT: fCAT

Description

Determine if a core gene was ignored by the tool because of the unknown references species

Usage

filterIgnore(root, coreSet, coreGene, priorityList)

Arguments

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
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.

Value

TRUE or FALSE

Examples

coreFolder <- system.file("extdata", "sample", package = "fCAT")
check <- filterIgnore(coreFolder, "test", "530670", c("HUMAN@9606@1"))
print(check)

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