PseKRAAC_T8 {ftrCOOL} | R Documentation |
Pseudo K_tuple Reduced Amino Acid Composition Type-8 (PseKRAAC_T8)
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_type8(PseKRAAC_T8) contains Grp 2-20.
Usage
PseKRAAC_T8(
seqs,
type = "gap",
Grp = 5,
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('ADEGKNPQRST', 'CFHILMVWY'), Grp3=c('ADEGNPST', 'CHKQRW', 'FILMVY'), Grp4=c('AGNPST', 'CHWY', 'DEKQR', 'FILMV'), Grp5=c('AGPST', 'CFWY', 'DEN', 'HKQR', 'ILMV'), Grp6=c('APST', 'CW', 'DEGN', 'FHY', 'ILMV', 'KQR'), Grp7=c('AGST', 'CW', 'DEN', 'FY', 'HP', 'ILMV', 'KQR'), Grp8=c('AST', 'CG', 'DEN', 'FY', 'HP', 'ILV', 'KQR', 'MW'), Grp9=c('AST', 'CW', 'DE', 'FY', 'GN', 'HQ', 'ILV', 'KR', 'MP'), Grp10=c('AST', 'CW', 'DE', 'FY', 'GN', 'HQ', 'IV', 'KR', 'LM', 'P'), Grp11=c('AST', 'C', 'DE', 'FY', 'GN', 'HQ', 'IV', 'KR', 'LM', 'P', 'W'), Grp12=c('AST', 'C', 'DE', 'FY', 'G', 'HQ', 'IV', 'KR', 'LM', 'N', 'P', 'W'), Grp13=c('AST', 'C', 'DE', 'FY', 'G', 'H', 'IV', 'KR', 'LM', 'N', 'P', 'Q', 'W'), Grp14=c('AST', 'C', 'DE', 'FL', 'G', 'H', 'IV', 'KR', 'M', 'N', 'P', 'Q', 'W', 'Y'), Grp15=c('AST', 'C', 'DE', 'F', 'G', 'H', 'IV', 'KR', 'L', 'M', 'N', 'P', 'Q', 'W', 'Y'), Grp16=c('AT', 'C', 'DE', 'F', 'G', 'H', 'IV', 'KR', 'L', 'M', 'N', 'P', 'Q', 'S', 'W', 'Y'), Grp17=c('AT', 'C', 'DE', 'F', 'G', 'H', 'IV', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'W', 'Y'), Grp18=c('A', 'C', 'DE', 'F', 'G', 'H', 'IV', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'W', 'Y'), Grp19=c('A', 'C', 'D', 'E', 'F', 'G', 'H', 'IV', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'W', 'Y'), Grp20=c('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'V', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'W', 'Y')
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_T8(seqs=filePrs,type="gap",Grp=4,GapOrLambdaValue=3,k=2)
mat2<-PseKRAAC_T8(seqs=filePrs,type="lambda",Grp=4,GapOrLambdaValue=3,k=2)