ExpectedValueAA {ftrCOOL}

Expected Value for each Amino Acid (ExpectedValueAA)

Description

This function is introduced by this package for the first time. It computes the expected value for each k-mer in a sequence. ExpectedValue(k-mer) = freq(k-mer) / (c_1 * c_2 * ... * c_k), where c_i is the number of codons that encrypt the i'th amino acid in the k-mer.

Usage

ExpectedValueAA(seqs, k = 2, normalized = TRUE, 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.

k

is an integer value. The default is two.

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 20^k.

Examples

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
mat<-ExpectedValueAA(seqs=filePrs,k=2,normalized=FALSE)