ftrCOOL (version 0.1.0)

ENUComposition: Enhanced nucleotide Composition

Description

This function slides a window over the input sequence(s). Also, it computes the composition of nucleotides that appears within the limits of the window. Please note that when a feature vector of sequences is given as the input, their length should be equal. Otherwise, either an error (in case the outFortmat is 'mat') or a text file (when the outFortmat is 'txt') is returned. Please note that the text file is not suitable for machine learning purposes.

Usage

ENUComposition(
  seqs,
  winSize = 20,
  overLap = TRUE,
  outFormat = "mat",
  outputFileDist = "",
  label = c()
)

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.

winSize

is a number which shows the size of the window.

overLap

This parameter shows how the window moves on the sequence. If the overlap is set to TRUE, the next window would have distance 1 with the previous window. Otherwise, the next window will start from the next amino acid after the previous window. There is no overlap between the next and previous windows.

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.

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

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 (4 * number of partitions displayed by the window) and the number of rows is equal to the number of sequences. It is usable for machine learning purposes. If the outFormat is 'txt', the output is written to a tab-delimited file.

Examples

# NOT RUN {
dir = tempdir()
LNCSeqsADR<-system.file("extdata/",package="ftrCOOL")
LNC50Nuc<-as.vector(read.csv(paste0(LNCSeqsADR,"/LNC50Nuc.csv"))[,2])
mat<-ENUComposition(seqs = LNC50Nuc, winSize=20,outFormat="mat")

ad<-paste0(dir,"/ENUCcompos.txt")
fileLNC<-system.file("extdata/Athaliana_LNCRNA.fa",package="ftrCOOL")
ENUComposition(seqs = fileLNC,outFormat="txt",winSize=20
,outputFileDist=ad,overLap=FALSE)
# }