SSEC: Secondary Structure Elements Composition (SSEC)
In ftrCOOL: Feature Extraction from Biological Sequences
Description
Usage
Arguments
Value
Examples
Description
This function works based on the output of PSIPRED which predicts the secondary structure of the amino acids in a sequence.
The output of the PSIPRED is a tab-delimited file which contains the secondary structure in the third column.
SSEC returns the frequency of the secondary structures (i.e., Helix, Extended, Coil) of the sequences.
Usage
1
SSEC(dirPath)
Arguments
dirPath
Path of the directory which contains all output files of PSIPRED. Each file belongs to a sequence.
Value
It returns a feature matrix which the number of rows is the number of sequences and
the number of columns is 3. The first column shows the number of amino acids which participate
in the coil structure. The second column shows the number of amino acids in the extended structure
and the last column shows the number of amino acids in the helix structure.
Examples
1
2
3
Predss2dir<-system.file("testForder",package="ftrCOOL")
Predss2dir<-paste0(Predss2dir,"/ss2Dir/")
mat<-SSEC(Predss2dir)
ftrCOOL documentation built on Nov. 30, 2021, 1:07 a.m.
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Description Usage Arguments Value Examples
Description
This function works based on the output of PSIPRED which predicts the secondary structure of the amino acids in a sequence. The output of the PSIPRED is a tab-delimited file which contains the secondary structure in the third column. SSEC returns the frequency of the secondary structures (i.e., Helix, Extended, Coil) of the sequences.
Usage
1 | SSEC(dirPath)
|
Arguments
dirPath |
Path of the directory which contains all output files of PSIPRED. Each file belongs to a sequence. |
Value
It returns a feature matrix which the number of rows is the number of sequences and the number of columns is 3. The first column shows the number of amino acids which participate in the coil structure. The second column shows the number of amino acids in the extended structure and the last column shows the number of amino acids in the helix structure.
Examples
1 2 3 | Predss2dir<-system.file("testForder",package="ftrCOOL")
Predss2dir<-paste0(Predss2dir,"/ss2Dir/")
mat<-SSEC(Predss2dir)
|
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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