GC.content: GC content

In vhcub: Virus-Host Codon Usage Co-Adaptation Analysis

Description

Calculates overall GC content as well as GC at first, second, and third codon positions.

Usage

GC.content(df.virus)

Arguments

df.virus

data frame with seq_name and its DNA sequence.

Value

A data.frame with overall GC content as well as GC at first, second, and third codon positions of all DNA sequence from df.virus.

Author(s)

Ali Mostafa Anwar [e-mail] and Mohmed Soudy [e-mail]

Examples

# read DNA from fasta file
fasta <- fasta.read("virus.fasta", "host.fasta")
fasta.v <- fasta[[1]]
fasta.h <- fasta[[2]]


# Calculate GC content
gc.df <- GC.content(fasta.v)

vhcub documentation built on Nov. 15, 2019, 5:10 p.m.