EAAComposition {ftrCOOL}

Enhanced Amino Acid Composition (EAAComposition)

Description

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

Usage

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

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.

winSize

is a number which shows the size of the window.

overLap

This parameter shows how the window moves over the sequence. If overlap is set to FALSE, the window slides over the sequence in such a way that every time the window moves, it covers a unique portion of the sequence. Otherwise, portions of the sequence which appear within the window limits have "winSize-1" amino acids in common.

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

Column names in the output matrix are Wi(aa), where aa shows an amino acid type ("A", "C", "D",..., "Y") and i indicates the number of times that the window has moved over the sequence(s).

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 (20 * 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.

When overlap is FALSE, the last partition represented by the window may have a different length with other parts.

References

Chen, Zhen, et al. "iFeature: a python package and web server for features extraction and selection from protein and peptide sequences." Bioinformatics 34.14 (2018): 2499-2502.

Examples

dir = tempdir()
ptmSeqsADR<-system.file("extdata/",package="ftrCOOL")
ptmSeqsVect<-as.vector(read.csv(paste0(ptmSeqsADR,"/ptmVect101AA.csv"))[,2])
mat<-EAAComposition(seqs = ptmSeqsVect,winSize=50, overLap=FALSE,outFormat='mat')

ad<-paste0(dir,"/EaaCompos.txt")
filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
EAAComposition(seqs = filePrs,winSize=50, overLap=FALSE,outFormat="txt"
,outputFileDist=ad)

unlink("dir", recursive = TRUE)