computePhysChem_AAindex: Computation of the AAindex-Based Physicochemical Features of...

In HAN-Siyu/ncProR: Predicting Long non-coding RNA-Protein Interaction

Computation of the AAindex-Based Physicochemical Features of Protein Sequences

Description

The function computePhysChem_AAindex computes the physicochemical features of protein sequences with the help of AAindex provided by aaindex from seqinr-package.

Usage

computePhysChem_AAindex(
  seqPro,
  entry.index = NULL,
  Fourier.len = 10,
  parallel.cores = 2,
  cl = NULL
)

Arguments

seqPro	protein sequences loaded by function read.fasta from seqinr-package. Each sequence should be a vector of single characters.
entry.index	The entry number of AAindex. For example the entry number of "Kyte & Doolittle Hydrophaty" index is 151, and the entry number of "Hopp-Woods Hydrophilicity" is 115. Thus, the corresponding entry.index is c(151, 115) for these two physicochemical indices. See examples and aaindex of "seqinr" package.
Fourier.len	positive integer specifying the Fourier series length that will be used as features. The Fourier.len should be >= the length of the input sequence. Default: 10.
parallel.cores	an integer that indicates the number of cores for parallel computation. Default: 2. Set parallel.cores = -1 to run with all the cores. parallel.cores should be == -1 or >= 1.
cl	parallel cores to be passed to this function.

Value

This function returns a data frame.

References

[1] Kawashima S, Kanehisa M. AAindex: amino acid index database. Nucleic Acids Res. 2000; 28:374

[2] Charif D, Lobry JR. SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. In: Structural approaches to sequence evolution: Molecules, networks, populations. 2007; 207-232

See Also

computePhysChem, aaindex

Examples

data(demoPositiveSeq)
seqs <- demoPositiveSeq$Pro.positive
data(aaindex, package = "seqinr")

# Check the aaindex list provided by package "seqinr":

?seqinr::aaindex

# Supose that we need "Kyte & Doolittle Hydrophaty" index,
# and we can find the entries with Kyte as author:

which(sapply(aaindex, function(x) length(grep("Kyte", x$A)) != 0))

# This returns entry number 151.
# And 151 is the "entry.index" used by this function.
# Users can also obtain the entry number by retrieving information in other
# fields such as "x$D" (Data description) or "x$T" (Title of the article).
# See documentation of "seqinr::aaindex" for detailed information.

feature_aaindex_1 <- computePhysChem_AAindex(seqPro = seqs, entry.index = 151,
                                             Fourier.len = 10, parallel.cores = 2)

# If you need to compute features with more than aaindex data:

feature_aaindex_2 <- computePhysChem_AAindex(seqPro = seqs, entry.index = c(151, 68),
                                             Fourier.len = 10, parallel.cores = 2)

HAN-Siyu/ncProR documentation built on Nov. 3, 2023, 12:08 a.m.