compute_hexamerScore {LncFinder}

Compute Hexamer Score

Description

This function can compute hexamer score proposed by method CPAT (Wang et al. 2013). Hexamer score can be calculated on full sequence or the longest ORF region. The step and k of the sliding window can also be customized.

Usage

compute_hexamerScore(
  Sequences,
  label = NULL,
  referFreq,
  k = 6,
  step = 1,
  alphabet = c("a", "c", "g", "t"),
  on.ORF = FALSE,
  auto.full = FALSE,
  parallel.cores = 2
)

Arguments

Sequences

A FASTA file loaded by function read.fasta of seqinr-package.

label

Optional. String. Indicate the label of the sequences such as "NonCoding", "Coding".

referFreq

A list obtained from function make_referFreq.

k

An integer that indicates the sliding window size. (Default: 6)

step

Integer defaulting to 1 for the window step.

alphabet

A vector of single characters that specify the different character of the sequence. (Default: alphabet = c("a", "c", "g", "t"))

on.ORF

Logical. If TRUE, hexamer score will be calculated on the longest ORF region. NOTE: If TRUE, the input has to be DNA sequences. (Default: FALSE)

auto.full

Logical. When on.ORF = TRUE but no ORF can be found, if auto.full = TRUE, hexamer score will be calculated on full sequences automatically; if auto.full is FALSE, the sequences that have no ORF will be discarded. Ignored when on.ORF = FALSE. (Default: FALSE)

parallel.cores

Integer. The number of cores for parallel computation. By default the number of cores is 2. Users can set as -1 to run this function with all cores.

Details

This function can compute hexamer score proposed by CPAT (Wang et al. 2013). In CPAT, hexamer score is calculated on the longest ORF region, and the step of the sliding window is 3 (i.e. step = 3). Hexamer means six adjoining bases, thus k = 6. But in function compute_hexamerScore, both step, k, and calculated region (full sequence or ORF) can be customized to maximize its availability.

Value

A dataframe.

References

Liguo Wang, Hyun Jung Park, Surendra Dasari, Shengqin Wang, JeanPierre Kocher, & Wei Li. CPAT: coding-potential assessment tool using an alignment-free logistic regression model. Nucleic Acids Research, 2013, 41(6):e74-e74.

Siyu Han, Yanchun Liang, Qin Ma, Yangyi Xu, Yu Zhang, Wei Du, Cankun Wang & Ying Li. LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information, and physicochemical property. Briefings in Bioinformatics, 2019, 20(6):2009-2027.

Author(s)

HAN Siyu

See Also

make_referFreq, compute_LogDistance, compute_EucDistance.

Examples

## Not run: 
Seqs <- seqinr::read.fasta(file =
"http://www.ncbi.nlm.nih.gov/WebSub/html/help/sample_files/nucleotide-sample.txt")

referFreq <- make_referFreq(cds.seq = Seqs, lncRNA.seq = Seqs, k = 6, step = 1,
                            alphabet = c("a", "c", "g", "t"), on.orf = TRUE,
                            ignore.illegal = TRUE)

data(demo_DNA.seq)
Sequences <- demo_DNA.seq

hexamerScore <- compute_hexamerScore(Sequences, label = "NonCoding", referFreq = referFreq,
                                     k = 6, step = 1, alphabet = c("a", "c", "g", "t"),
                                     on.ORF = TRUE, auto.full = TRUE, parallel.cores = 2)

## End(Not run)