PseKRAAC_T3A {ftrCOOL}

Pseudo K_tuple Reduced Amino Acid Composition Type-3A (PseKRAAC_T3A)

Description

There are 16 types of PseKRAAC function. In the functions, a (user-selected) grouping of the amino acids might be used to reduce the amino acid alphabet. Also, the functions have a type parameter. The parameter determines the protein sequence analyses which can be either gap or lambda-correlation. PseKRAAC_type3 contain two type: type3A and type3B. 'PseKRAAC_T3A' contains Grp 2-20.

Usage

PseKRAAC_T3A(
  seqs,
  type = "gap",
  Grp = 2,
  GapOrLambdaValue = 2,
  k = 4,
  label = c()
)

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.

type

This parameter has two valid value "lambda" and "gap". "lambda" calls lambda_model function and "gap" calls gap_model function.

Grp

is a numeric value. It shows the id of an amino acid group. Please find the available groups in the detail section.

GapOrLambdaValue

is an integer. If type is gap, this value shows number of gaps between two k-mers. If type is lambda, the value of GapOrLambdaValue shows the number of gaps between each two amino acids of k-mers.

k

This parameter keeps the value of k in k-mer.

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).

Details

Groups: Grp2=c('AGSPDEQNHTKRMILFYVC', 'W'), Grp3=c('AGSPDEQNHTKRMILFYV', 'W', 'C'), Grp4=c('AGSPDEQNHTKRMIV', 'W', 'YFL', 'C'), Grp5=c('AGSPDEQNHTKR', 'W', 'YF', 'MIVL', 'C'), Grp6=c('AGSP', 'DEQNHTKR', 'W', 'YF', 'MIL', 'VC'), Grp7=c('AGP', 'DEQNH', 'TKRMIV', 'W', 'YF', 'L', 'CS'), Grp8=c('AG', 'DEQN', 'TKRMIV', 'HY', 'W', 'L', 'FP', 'CS'), Grp9=c('AG', 'P', 'DEQN', 'TKRMI', 'HY', 'W', 'F', 'L', 'VCS'), Grp10=c('AG', 'P', 'DEQN', 'TKRM', 'HY', 'W', 'F', 'I', 'L', 'VCS'), Grp11=c('AG', 'P', 'DEQN', 'TK', 'RI', 'H', 'Y', 'W', 'F', 'ML', 'VCS'), Grp12=c('FAS', 'P', 'G', 'DEQ', 'NL', 'TK', 'R', 'H', 'W', 'Y', 'IM', 'VC'), Grp13=c('FAS', 'P', 'G', 'DEQ', 'NL', 'T', 'K', 'R', 'H', 'W', 'Y', 'IM', 'VC'), Grp14=c('FA', 'P', 'G', 'T', 'DE', 'QM', 'NL', 'K', 'R', 'H', 'W', 'Y', 'IV', 'CS'), Grp15=c('FAS', 'P', 'G', 'T', 'DE', 'Q', 'NL', 'K', 'R', 'H', 'W', 'Y', 'M', 'I', 'VC'), Grp16=c('FA', 'P', 'G', 'ST', 'DE', 'Q', 'N', 'K', 'R', 'H', 'W', 'Y', 'M', 'L', 'I', 'VC'), Grp17=c('FA', 'P', 'G', 'S', 'T', 'DE', 'Q', 'N', 'K', 'R', 'H', 'W', 'Y', 'M', 'L', 'I', 'VC'), Grp18=c('FA', 'P', 'G', 'S', 'T', 'DE', 'Q', 'N', 'K', 'R', 'H', 'W', 'Y', 'M', 'L', 'I', 'V', 'C'), Grp19=c('FA', 'P', 'G', 'S', 'T', 'D', 'E', 'Q', 'N', 'K', 'R', 'H', 'W', 'Y', 'M', 'L', 'I', 'V', 'C'), Grp20=c('F', 'A', 'P', 'G', 'S', 'T', 'D', 'E', 'Q', 'N', 'K', 'R', 'H', 'W', 'Y', 'M', 'L', 'I', 'V', 'C')

Value

This function returns a feature matrix. The number of rows is equal to the number of sequences and the number of columns is (Grp)^k.

References

Zuo, Yongchun, et al. "PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition." Bioinformatics 33.1 (2017): 122-124.

Examples

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")

mat1<-PseKRAAC_T3A(seqs=filePrs,type="gap",Grp=4,GapOrLambdaValue=3,k=2)

mat2<-PseKRAAC_T3A(seqs=filePrs,type="lambda",Grp=4,GapOrLambdaValue=3,k=2)