calculateBuscoCutoff: The function to calculate the cutoff value based on standard...
In giangnguyen0709/fCAT: fCAT
Description
Usage
Arguments
Value
Examples
Description
The function to calculate the cutoff value based on standard deviation of
the length for each core group. This function will be used in score mode
"busco"
Usage
1
calculateBuscoCutoff(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
Value
a list that contains the mean length and the standard deviation of
the length of the core gene
Examples
1
2
3
coreFolder <- system.file("extdata", "sample", package = "fCAT")
cutoff <- calculateBuscoCutoff(coreFolder, "test", "530670")
print(cutoff)
giangnguyen0709/fCAT documentation built on Feb. 10, 2021, 4:31 a.m.
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Description Usage Arguments Value Examples
Description
The function to calculate the cutoff value based on standard deviation of the length for each core group. This function will be used in score mode "busco"
Usage
1 | calculateBuscoCutoff(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 |
Value
a list that contains the mean length and the standard deviation of the length of the core gene
Examples
1 2 3 | coreFolder <- system.file("extdata", "sample", package = "fCAT")
cutoff <- calculateBuscoCutoff(coreFolder, "test", "530670")
print(cutoff)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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