ENUComposition_RNA {ftrCOOL}

Enhanced riboNucleotide Composition (ENUComposition_RNA)

Description

This function slides a window over the input sequence(s). Also, it computes the composition of ribonucleotides that appears within the limits of the window.

Usage

ENUComposition_RNA(
  seqs,
  winSize = 50,
  overLap = TRUE,
  label = c(),
  outFormat = "mat",
  outputFileDist = ""
)

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.

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 ribonucleotide after the previous window. There is no overlap between the next and previous windows.

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.

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. 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

dir = tempdir()
LNCSeqsADR<-system.file("extdata/",package="ftrCOOL")
fileLNC<-system.file("extdata/Carica_papaya101RNA.txt",package="ftrCOOL")
mat<-ENUComposition_RNA(seqs = fileLNC, winSize=20,outFormat="mat")

ad<-paste0(dir,"/ENUCcompos.txt")
ENUComposition_RNA(seqs = fileLNC,outFormat="txt",winSize=20
,outputFileDist=ad,overLap=FALSE)


unlink("dir", recursive = TRUE)