This function calculates the grouped tripeptide composition with conjoint
triad grouping type. For each k, it creates a 7^3 feature vector.
K is the space between the first and the second amino acids
and the second and the third amino acids of the tripeptide.
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.
rng
This parameter can be a number or a vector. Each element of the vector shows the number of spaces between the first and the second amino acids
and the second and the third amino acids of the tripeptide.
For each k in the rng vector, a new vector (whose size is 7^3) is created which contains the frequency of tri-amino acid with k gaps.
upto
It is a logical parameter. The default value is FALSE. If rng is a number and upto is set to TRUE, rng is converted
to a vector with values from 0 to rng.
normalized
is a logical parameter. When it is FALSE, the return value of the function does not change. Otherwise, the return value is normalized using the length of the sequence.
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).
Value
This function returns a feature matrix. The number of rows is equal to the number of sequences and
the number of columns is (7^3)*(length rng vector).
Details
A tripeptide with k spaces looks like AA1(ss..s)AA2(ss..s)AA3. AA stands for amino acids and s means space.
# NOT RUN {filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
mat1<-conjointTriadKS(filePrs,rng=2,upto=TRUE,normalized=TRUE)
mat2<-conjointTriadKS(filePrs,rng=c(1,3,5))
# }