calculateCutoff: The function calculate all cutoff values for all mode of a...

In giangnguyen0709/fCAT: fCAT

Description

The function calculate all cutoff values for all mode of a specific core gene in the set. For score mode 1 it will calculate the avarage of all vs all FAS scores between the training sequences in the core gene. For score mode 2 it will calculate the avarage of the FAS score between each sequence against all training sequences in the core gene. The scores will be writen in a table with a column is the ID of the sequences and a column is the corresponding value. For score mode 3, the function will calculate the avarage of 1 vs all FAS scores for each training sequence in the core gene. The avarages build a distribution, the function will calculate the confidence interval of this distribution and write the upper value and the lower value of the interval in a file in the core gene folder.

Usage

calculateCutoff(root, coreSet, coreGene)

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 in the set

Value

none

Examples

coreFolder <- system.file("extdata", "sample", package = "fCAT")
calculateCutoff(coreFolder, "test", "530670")

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