compute_pI: Compute Theoretical Isoelectric Point
In LncFinder: LncRNA Identification and Analysis Using Heterologous Features

compute_pI

R Documentation

Compute Theoretical Isoelectric Point

Description

This function is basically a wrapper for function computePI. This function translate DNA sequence into protein, and compute the theoretical isoelectric point (pI) of this protein.

Usage

compute_pI(
  Sequences,
  label = NULL,
  on.ORF = FALSE,
  auto.full = FALSE,
  ambiguous.base = 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".
`on.ORF`	Logical. If `TRUE`, pI 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`, pI 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`)
`ambiguous.base`	If `TRUE`, ambiguous bases are taken into account when translating DNA sequences into proteins.
`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 the pI of DNA sequences. Method CPC2 (Kang et al. 2017) uses this feature to identify lncRNAs, and this feature is evaluated in the article LncFinder (Han et al. 2018).

Using this function, the theoretical pI can be computed on full sequence or the longest ORF region. In CPC2, pI is calculated on ORF region.

Value

A dataframe.

Author(s)

HAN Siyu

Examples

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

pI_res <- compute_pI(Sequences, on.ORF = TRUE, auto.full = FALSE, ambiguous.base = FALSE)

## End(Not run)

LncFinder documentation built on Sept. 29, 2024, 1:06 a.m.