Extract: A feature extractor function.

In g1o/GeneEssentiality: Gene essentiality predictor

Description

Input a DNA fasta file and it will output a vector of features for each sequence.

Usage

Extract(
  FASTA_PATH = "",
  AAfile = "",
  PFAM_path = "",
  LAMBDA = 50,
  OMEGA = 0.05,
  CPU = 2,
  nuc_only = F,
  varGibbs_Model_path = "/mnt/DATABASES/bin/VarGibbs-2.2/data/AOP-CMB.par",
  subcel = F
)

Arguments

FASTA_PATH	Path to the DNA fasta file.
PFAM_path	Path to the PfamA database.
LAMBDA	Pseudo amino acid composition parameter. Sequences with less amino acids than LAMBDA will be removed (50).
OMEGA	Pseudo amino acid composition parameter (0.05).
CPU	Number of threads to use. Each sequence will use one thread (2).
subcel	use DeepLoc1.0 to predict probabilities for subcellular localization (F)

Value

A data frame of features

g1o/GeneEssentiality documentation built on Jan. 3, 2022, 1:21 a.m.