LncFinder (version 1.1.6)

compute_EIIP: Extract the EIIP-derived features

Description

This function can extract EIIP-derived features proposed by Han et al (2018).

Usage

compute_EIIP(
  Sequences,
  label = NULL,
  spectrum.percent = 0.1,
  quantile.probs = seq(0, 1, 0.25)
)

Value

A dataframe including the EIIP-derived features.

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".

spectrum.percent

Numeric specifying the percentage of the sorted power spectrum that be used to calculate the quantile-based features. For example, if spectrum.percent = 0.1, the top 10% percent of the sorted power spectrum will be used to compute the quantiles.

quantile.probs

Numeric. The probabilities with values in [0,1].

Author

HAN Siyu

Details

The function compute_EIIP can extract EIIP (electron-ion interaction pseudo-potential) features including: signal at 1/3 position (Signal.Peak), average power (Average.Power), signal to noise ratio (SNR), and quantile-based features of one specified percentage of the sorted power spectrum (e.g. 0%, 20%, 40%, 60%, 70%, 100% when quantile.probs = seq(0, 1, 0.2) and spectrum.percent = 0.1).

In method LncFinder, EIIP features includes Signal.Peak, SNR, 0% (Signal.Min), 25% (Singal.Q1, 50% Signal.Q2), and 75% (Signal.Max) of the top 10% sorted power spectrum, i.e. quantile.prob = seq(0, 1, 0.25) and spectrum.percent = 0.1.

References

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.

Please cite the following paper, which originally proposed EIIP:

Lalović, Dragutin, and Veljko Veljković. The global average DNA base composition of coding regions may be determined by the electron-ion interaction potential. Biosystems, 1990, 23(4):311-316.

See Also

extract_features

Examples

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

EIIP_res <- compute_EIIP(Seqs, label = "NonCoding", spectrum.percent = 0.25,
                         quantile.probs = seq(0, 1, 0.25))