GrpDDE: Group Dipeptide Deviation from Expected Mean (GrpDDE)

In ftrCOOL: Feature Extraction from Biological Sequences

Description

This function is introduced by this package for the first time. In this function, amino acids are first grouped into user-defined categories. Later, DDE is applied to grouped amino acids. Please note that this function differs from DDE which works on individual amino acids.

Usage

GrpDDE(seqs, Grp = "locFus", label = c())

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.
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).

Value

A feature matrix with (number of categorizes)^2 number of columns. The number of rows is equal to the number of sequences.

Examples

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
mat1<-GrpDDE(seqs=filePrs,Grp="aromatic")

mat2<-GrpDDE(seqs=filePrs,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")))

ftrCOOL documentation built on Nov. 30, 2021, 1:07 a.m.