EGAAComposition {ftrCOOL}

Enhanced Grouped Amino Acid Composition (EGAAComposition)

Description

In this function, amino acids are first grouped into user-defined categories. Then, enhanced grouped amino acid composition is computed. For details about the enhanced feature, please refer to function EAAComposition. Please note that this function differs from function EAAComposition which works on individual amino acids.

Usage

EGAAComposition(
  seqs,
  winSize = 50,
  overLap = TRUE,
  Grp = "locFus",
  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

shows the size of sliding window. It is a numeric value.

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.

Grp

is a list of vectors containig amino acids. Each vector represents a category. Users can define a customized amino acid grouping, provided that the sum of all amino acids is 20 and there is no repeated amino acid in the groups. Also, users can choose 'cTriad'(conjointTriad), 'locFus', or 'aromatic'. Each option provides specific information about the type of an amino acid grouping.

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 ((number of categorizes) * (number of windows)) 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])
mat1<-EGAAComposition(seqs = ptmSeqsVect,winSize=20,overLap=FALSE,Grp="locFus")

mat2<-EGAAComposition(seqs = ptmSeqsVect,winSize=30,overLap=FALSE,Grp=
list(Grp1=c("G","A","V","L","M","I","F","Y","W"),Grp2=c("K","R","H","D","E")
,Grp3=c("S","T","C","P","N","Q")),outFormat="mat")

ad<-paste0(dir,"/EGrpaaCompos.txt")
filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
EGAAComposition(seqs = filePrs,winSize=20,Grp="cTriad",outFormat="txt"
,outputFileDist=ad)


unlink("dir", recursive = TRUE)