PseKRAAC_T16 {ftrCOOL} | R Documentation |
Pseudo K_tuple Reduced Amino Acid Composition Type-16 (PseKRAAC_T16)
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_type16(PseKRAAC_T16) contains Grp 2-16,20.
Usage
PseKRAAC_T16(
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:
2=c('IMVLFWY', 'GPCASTNHQEDRK'), 3=c('IMVLFWY', 'GPCAST', 'NHQEDRK'), 4=c('IMVLFWY', 'G', 'PCAST', 'NHQEDRK'), 5=c('IMVL', 'FWY', 'G', 'PCAST', 'NHQEDRK'), 6=c('IMVL', 'FWY', 'G', 'P', 'CAST', 'NHQEDRK'), 7=c('IMVL', 'FWY', 'G', 'P', 'CAST', 'NHQED', 'RK'), 8=c('IMV', 'L', 'FWY', 'G', 'P', 'CAST', 'NHQED', 'RK'), 9=c('IMV', 'L', 'FWY', 'G', 'P', 'C', 'AST', 'NHQED', 'RK'), 10=c('IMV', 'L', 'FWY', 'G', 'P', 'C', 'A', 'STNH', 'RKQE', 'D'), 11=c('IMV', 'L', 'FWY', 'G', 'P', 'C', 'A', 'STNH', 'RKQ', 'E', 'D'), 12=c('IMV', 'L', 'FWY', 'G', 'P', 'C', 'A', 'ST', 'N', 'HRKQ', 'E', 'D'), 13=c('IMV', 'L', 'F', 'WY', 'G', 'P', 'C', 'A', 'ST', 'N', 'HRKQ', 'E', 'D'), 14=c('IMV', 'L', 'F', 'WY', 'G', 'P', 'C', 'A', 'S', 'T', 'N', 'HRKQ', 'E', 'D'), 15=c('IMV', 'L', 'F', 'WY', 'G', 'P', 'C', 'A', 'S', 'T', 'N', 'H', 'RKQ', 'E', 'D'), 16=c('IMV', 'L', 'F', 'W', 'Y', 'G', 'P', 'C', 'A', 'S', 'T', 'N', 'H', 'RKQ', 'E', 'D'), 20=c('I', 'M', 'V', 'L', 'F', 'W', 'Y', 'G', 'P', 'C', 'A', 'S', 'T', 'N', 'H', 'R', 'K', 'Q', 'E', 'D')
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_T16(seqs=filePrs,type="gap",Grp=4,GapOrLambdaValue=3,k=2)
mat2<-PseKRAAC_T16(seqs=filePrs,type="lambda",Grp=4,GapOrLambdaValue=3,k=2)