TPCP_DNA {ftrCOOL}

Trinucleotide physicochemical properties (TPCP_DNA)

Description

This function replaces trinucleotides in a sequence with their physicochemical properties which is multiplied by normalized frequency of that tri-nucleotide.

Usage

TPCP_DNA(
  seqs,
  selectedIdx = c("Dnase I", "Bendability (DNAse)"),
  threshold = 1,
  label = c(),
  outFormat = "mat",
  outputFileDist = ""
)

Arguments

seqs

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

selectedIdx

TPCP_DNA function works based on physicochemical properties. Users, select the properties by their ids or indexes in TRI_DNA index file. The default values of the vector are the ids in "Dnase I", "Bendability (DNAse)".

threshold

is a number between 0 to 1. In selectedIdx, indices with a correlation higher than the threshold will be deleted. The default value is 1.

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).

outFormat

(output format) can take two values: 'mat'(matrix) and 'txt'. The default value is 'mat'.

outputFileDist

shows the path and name of the 'txt' output file.

Details

There are 12 physicochemical indexes in the trinucleotide database.

Value

The output depends on the outFormat parameter which can be either 'mat' or 'txt'. If outFormat is 'mat', the function returns a feature matrix for sequences with the same length such that the number of columns is (sequence length-2)*(number of selected trinucleotide properties) and the number of rows is equal to the number of sequences. If the outFormat is 'txt', the output is written to a tab-delimited file.

Note

This function is provided for sequences with the same lengths. Users can use 'txt' option in outFormat for sequences with different lengths. Warning: If outFormat is set to 'mat' for sequences with different lengths, it returns an error. Also, when output format is 'txt', label information is not shown in the text file. It is noteworthy that 'txt' format is not usable for machine learning purposes if sequences have different sizes. Otherwise 'txt' format is also usable for machine learning purposes.

Examples

fileLNC<-system.file("extdata/Athaliana1.fa",package="ftrCOOL")
vect<-TPCP_DNA(seqs = fileLNC,threshold=1,outFormat="mat")