ftrCOOL (version 2.0.0)

PSTNPss_RNA: Position-Specific Tri-ribonucleotide Propensity based on single-strand RNA (PSTNPss_RNA)

Description

The inputs to this function are positive and negative data sets and a set of sequences. The output of the function is a matrix of feature vectors. The number of rows of the output matrix is equal to the number of sequences. The feature vector for an input sequence with length L is [u(1),u(2),...u(L-2)]. For each input sequence, u(1) is calculated by subtracting the frequency of sequences (which start with the same tri-ribonucleotides as the input sequence) in the positive set with those starting with the same tri-ribonucleotide in the negative set. We compute u(i) like u(1) with the exception that instead of the first tri-ribonucleotide, the ith tri-ribonucletide is considered.

Usage

PSTNPss_RNA(seqs, pos, neg, label = c())

Arguments

seqs

is a FASTA file containing ribonucleotide sequences. The sequences start with '>'. Also, seqs could be a string vector. Each element of the vector is a ribonucleotide sequence.

pos

is a fasta file containing ribonucleotide sequences. Each sequence starts with '>'. Also, the value of this parameter can be a string vector. The sequences are positive sequences in the training model

neg

is a fasta file containing ribonucleotide sequences. Each sequence starts with '>'. Also, the value of this parameter can be a string vector.

label

is an optional parameter. It is a vector whose length is equal to the number of sequences. It shows the class of each entry (i.e., sequence).

Value

It returns a feature matrix. The number of columns is equal to the length of sequences minus two and the number of rows is equal to the number of sequences.

Examples

# NOT RUN {

ptmSeqsADR<-system.file("extdata/",package="ftrCOOL")


posSeqs<-fa.read(file=paste0(ptmSeqsADR,"/pos2RNA.txt"),alphabet="rna")
negSeqs<-fa.read(file=paste0(ptmSeqsADR,"/neg2RNA.txt"),alphabet="rna")
seqs<-fa.read(file=paste0(ptmSeqsADR,"/testSeq2RNA.txt"),alphabet="rna")


PSTNPss_RNA(seqs=seqs,pos=posSeqs,neg=negSeqs)



# }