SSEB {ftrCOOL}

Secondary Structure Elements Binary (SSEB)

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. SSEB gives a binary number (i.e., '001'='H','010'=E','100'='C') for each amino acid.

Usage

SSEB(dirPath, binaryType = "numBin", outFormat = "mat", outputFileDist = "")

Arguments

dirPath

Path of the directory which contains all output files of PSIPRED. Each file belongs to a sequence.

binaryType

It can take any of the following values: ('strBin','logicBin','numBin'). 'strBin'(String binary): each structure is represented by a string containing 3 characters(0-1). Helix = "001" , Extended = "010" , coil = "100". 'logicBin'(logical value): Each structure is represented by a vector containing 3 logical entries. Helix = c(FALSE,FALSE,TRUE) , Extended = c(FALSE,TRUE,FALSE) , Coil = c(TRUE,FALSE,FALSE). 'numBin' (numeric bin): Each structure is represented by a numeric (i.e., integer) vector containing 3 numerals. Helix = c(0,0,1) , Extended = c(0,1,0) , coil = c(1,0,0).

outFormat

It can take two values: 'mat' (which stands for matrix) and 'txt'. The default value is 'mat'.

outputFileDist

It shows the path and name of the 'txt' output file.

Details

This function converts each amino acid to a 3-bit value, such that 2 bits are 0 and 1 bit is 1. The position of 1 shows the type of the secondary structure of the amino acids in the protein/peptide. In this function, '001' is used to show Helix structure, '010' to show Extended structure and '100' to show coil structure.

Value

The output is different depending on the outFormat parameter ('mat' or 'txt'). If outFormat is set to 'mat', it returns a feature matrix for sequences with the same lengths. The number of rows is equal to the number of sequences and if binaryType is 'strBin', the number of columns is the length of the sequences. Otherwise, it is equal to (length of the sequences)*3. If outFormat is 'txt', all binary values will be written to a tab-delimited file. Each line in the file shows the binary format of a sequence.

Note

This function is provided for sequences with the same lengths. Users can use 'txt' option in the outFormat parameter for sequences with different lengths. Warning: If the outFormat is set to 'mat' for sequences with different lengths, it returns an error. It is noteworthy that 'txt' format is not usable for machine learning purposes.

Examples

dir = tempdir()
ad<-paste0(dir,"/SSEB.txt")

Predss2dir<-system.file("testForder",package="ftrCOOL")
Predss2dir<-paste0(Predss2dir,"/ss2Dir/")
mat<-SSEB(Predss2dir,binaryType="numBin",outFormat="txt",outputFileDist=ad)

unlink("dir", recursive = TRUE)