calculateAutocor: Calculate Autocorrelation Descriptors

In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

Calculate Autocorrelation Descriptors

Description

This function calculates autocorrelation descriptors:

• moran - moran autocorrelation, (Dim: length(target.props) * nlag).

• geary - geary autocorrelation, (Dim: length(target.props) * nlag).

• moreaubroto - moreau-broto autocorrelation, (Dim: length(target.props) * nlag).

Usage

calculateAutocor(
  x,
  target.props = c("CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102",
    "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"),
  nlag = 30L,
  type = c("moran", "geary", "moreaubroto")
)

Arguments

x	A data.frame containing gene/protein names and their fasta sequences.
target.props	A character vector, specifying the accession number of the target properties. 8 properties are used by default, as listed below: AccNo. CIDH920105 Normalized average hydrophobicity scales (Cid et al., 1992) AccNo. BHAR880101 Average flexibility indices (Bhaskaran-Ponnuswamy, 1988) AccNo. CHAM820101 Polarizability parameter (Charton-Charton, 1982) AccNo. CHAM820102 Free energy of solution in water, kcal/mole (Charton-Charton, 1982) AccNo. CHOC760101 Residue accessible surface area in tripeptide (Chothia, 1976) AccNo. BIGC670101 Residue volume (Bigelow, 1967) AccNo. CHAM810101 Steric parameter (Charton, 1981) AccNo. DAYM780201 Relative mutability (Dayhoff et al., 1978b)
nlag	Maximum value of the lag parameter. Default is 30.
type	The autocorrelation type: moran, geary, or moreaubroto.

Details

calculateAutocor

Value

A length nlag named vector for data input.

Author(s)

Matineh Rahmatbakhsh <[e-mail]>, Nan Xiao

References

AAindex: Amino acid index database. http://www.genome.ad.jp/dbget/aaindex.html

Feng, Z.P. and Zhang, C.T. (2000) Prediction of membrane protein types based on the hydrophobic index of amino acids. Journal of Protein Chemistry, 19, 269-275.

Horne, D.S. (1988) Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities. Biopolymers, 27, 451-477.

Sokal, R.R. and Thomson, B.A. (2006) Population structure inferred by local spatial autocorrelation: an Usage from an Amerindian tribal population. American Journal of Physical Anthropology, 129, 121-131.

Examples

data(UP000464024_df)
x_df <- calculateAutocor(UP000464024_df,type = 'moran')
head(x_df, n = 2L)

mrbakhsh/HPiP documentation built on March 28, 2023, 4:35 p.m.