binary_3bit_T7 {ftrCOOL}

Binary - 3bit - Type7 (binary_3bit_T7)

Description

This group of functions(binary_3bit_T1-T7) categorizes amino acids in 3 groups based on the type. Then represent group of amino acids by a three dimentional vector. The type of the binary format is determined by the binaryType parameter. For details about each format, please refer to the description of the binaryType parameter.

Usage

binary_3bit_T7(
  seqs,
  binaryType = "numBin",
  label = c(),
  outFormat = "mat",
  outputFileDist = ""
)

Arguments

seqs

is a FASTA file with amino acid sequences. Each sequence starts with a '>' character. Also, seqs could be a string vector. Each element of the vector is a peptide/protein sequence.

binaryType

It can take any of the following values: ('strBin','logicBin','numBin'). 'strBin'(String binary): each amino acid is represented by a string containing 20 characters(0-1). For example, A = ALANIN = "1000000...0" 'logicBin'(logical value): Each amino acid is represented by a vector containing 20 logical entries. For example, A = ALANIN = c(T,F,F,F,F,F,F,...F) 'numBin' (numeric bin): Each amino acid is represented by a numeric (i.e., integer) vector containing 20 numerals. For example, A = ALANIN = c(1,0,0,0,0,0,0,...,0)

label

is an optional parameter. It is a vector whose length is equivalent to the number of sequences. It shows the class of each entry (i.e., sequence).

outFormat

(output format) can take two values: 'mat'(matrix) and 'txt'. The default value is 'mat'.

outputFileDist

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

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 the output is 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 outFormat for sequences with different lengths. Warning: If outFormat is set to 'mat' for sequences with different lengths, it returns an error. Also, when output format is 'txt', label information is not shown in the text file. It is noteworthy that 'txt' format is not usable for machine learning purposes if sequences have different sizes. Otherwise 'txt' format is also usable for machine learning purposes.

Examples

ptmSeqsADR<-system.file("extdata/",package="ftrCOOL")
ptmSeqsVect<-as.vector(read.csv(paste0(ptmSeqsADR,"/ptmVect101AA.csv"))[,2])
mat<-binary_3bit_T7(seqs = ptmSeqsVect, binaryType="numBin",outFormat="mat")