CkSGAApair {ftrCOOL}

Composition of k-Spaced Grouped Amino Acids pairs (CkSGAApair)

Description

In this function, amino acids are first grouped into a category which is defined by the user. Later, the composition of the k-spaced grouped amino acids is computed. Please note that this function differs from CkSAApair which works on individual amino acids.

Usage

CkSGAApair(
  seqs,
  rng = 3,
  upto = FALSE,
  normalized = TRUE,
  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.

rng

This parameter can be a number or a vector. Each element of the vector shows the number of spaces between amino acid pairs. For each k in the rng vector, a new vector (whose size is (number of categorizes)^2) is created which contains the frequency of pairs with k gaps.

upto

It is a logical parameter. The default value is FALSE. If rng is a number and upto is set to TRUE, rng is converted to a vector with values from [1 to rng].

normalized

is a logical parameter. When it is FALSE, the return value of the function does not change. Otherwise, the return value is normalized using the length of the 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).

Details

Column names in the feature matrix follow G(?ss?). For example, G(1ss2) means Group1**Group2, where '*' is a wild character.

Value

This function returns a feature matrix. Row length is equal to the number of sequences and the number of columns is ((number of categorizes)^2)*(length of rng vector).

Note

'upto' is enabled only when rng is a number and not a vector.

Examples

filePrs<-system.file("extdata/proteins.fasta",package="ftrCOOL")
mat1<-CkSGAApair(seqs=filePrs,rng=2,upto=TRUE,Grp="aromatic")

mat2<-CkSGAApair(seqs=filePrs,rng=c(1,3,5),upto=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")))