| SSEC {ftrCOOL} | R Documentation |
Secondary Structure Elements Composition (SSEC)
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
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
Predss2dir<-system.file("testForder",package="ftrCOOL")
Predss2dir<-paste0(Predss2dir,"/ss2Dir/")
mat<-SSEC(Predss2dir)