Calc_feats: Calculate features of a sequence

In g1o/GeneEssentiality: Gene essentiality predictor

Description

Extract the features from a single nucleotide sequence. Also translate in the 3+ frames seaching for the longest ORF, using it to extract the features for the amino acid sequence.

Usage

Calc_feats(
  seq,
  aa = "",
  PFAM_PATH = "",
  LAMBDA = 50,
  OMEGA = 0.05,
  subcel = T,
  nuc_only = F,
  varGibbs_Model_PATH = "/mnt/DATABASES/bin/VarGibbs-2.2/data/AOP-CMB.par"
)

Arguments

seq	nucleotide sequence, works using a SeqFastadna object from the seqinr package.
PFAM_PATH	Path to the Pfam-A database
LAMBDA	Pseudo AA composition parameter
OMEGA	Pseudo AA composition parameter

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