compute_FickettScore: Compute Fickett TESTCODE Score
In LncFinder: LncRNA Identification and Analysis Using Heterologous Features

Description Usage Arguments Details Value References Author(s) Examples

This function can compute Fickett TESTCODE score of DNA sequences proposed by James W.Fickett (Fickett JW. 1982). Fickett TESTCODE score can be calculated on full sequence or the longest ORF region.

compute_FickettScore(
  Sequences,
  label = NULL,
  on.ORF = FALSE,
  auto.full = FALSE,
  parallel.cores = 2
)

`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".
`on.ORF`	Logical. If `TRUE`, Fickett TESTCODE score will be calculated on the longest ORF region.
`auto.full`	Logical. When `on.ORF = TRUE` but no ORF can be found, if `auto.full = TRUE`, Fickett TESTCODE 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.

This function can compute Fickett TESTCODE score proposed by James W.Fickett (Fickett JW. 1982). Fickett TESTCODE score is selected as feature by method CPAT (Wang et al. 2013) and CPC2 (Kang et al. 2017). In CPAT, Fickett TESTCODE score is calculated on the longest ORF region, but CPC2 calculates the score on full sequence. This function compute_FickettScore improves the CPAT's code and is capable of computing the score on the longest ORF region as well as full sequence.

A dataframe.

James W.Fickett. Recognition of protein coding regions in DNA sequences. Nucleic Acids Research, 1982, 10(17):5303-5318.

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.

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.

Yu-Jian Kang, De-Chang Yang, Lei Kong, Mei Hou, Yu-Qi Meng, Liping Wei & Ge Gao. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Research, 2017, 45(W1):W12-W16.

HAN Siyu

## Not run: 
data(demo_DNA.seq)
Seqs <- demo_DNA.seq

FickettScore <- compute_FickettScore(Seqs, label = NULL, on.ORF = TRUE,
                                     auto.full = TRUE, parallel.cores = 2)

## End(Not run)