AAindex {ftrCOOL}

Amino Acid Index (AAindex)

Description

This function converts the amino acids of a sequence to a list of physicochemical properties in the aaIndex file. For each amino acid, the function uses a numeric vector which shows the aaIndex of the amino acid.

Usage

AAindex(
  seqs,
  selectedAAidx = 1:554,
  standardized = TRUE,
  threshold = 1,
  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.

selectedAAidx

AAindex function works based on physicochemical properties. Users select the properties by their ids or indexes in aaIndex2 file.

standardized

is a logical parameter. If it is set to TRUE, amino acid indices will be in the standard format. The default value is TRUE.

threshold

is a number between (0 , 1]. In selectedAAidx, 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

In this function each amino acid is converted to a numeric vector. Elements of the vector represent a physicochemical property for the amino acid. In the aaIndex database, there are 554 amino acid indices. Users can choose the desired aaindex by specifying aaindexes through their ids or indexes in the aaIndex file, via selectedAAidx parameter.

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)*(number of selected amino acid indexes) 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()
ptmSeqsADR<-system.file("extdata/",package="ftrCOOL")
ptmSeqsVect<-as.vector(read.csv(paste0(ptmSeqsADR,"/ptmVect101AA.csv"))[,2])
mat<-AAindex(seqs = ptmSeqsVect, selectedAAidx=1:5,outFormat="mat")

ad<-paste0(dir,"/aaidx.txt")
filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
AAindex(seqs = filePrs, selectedAAidx=1:5,standardized=TRUE,threshold=1,outFormat="txt"
,outputFileDist=ad)

unlink("dir", recursive = TRUE)