vhcub (version 1.0.0)

CAI.values: Codon Adaptation Index (CAI)

Description

Measure the Codon Adaptation Index (CAI) Sharp and Li (1987), of DNA sequence.

Usage

CAI.values(df.virus, ENc.set.host,
                       df.host,genetic.code = "1",set.len = 5, threshold = 0)

Arguments

df.virus

a data frame with seq_name and its virus DNA sequence.

ENc.set.host

a data frame with ENc values of a host.

df.host

a data frame with seq_name and its host DNA sequence.

genetic.code

a single string that uniquely identifies a genetic code to use.

set.len

a number represents a percent that will be used as reference genes from the total host genes.

threshold

optional numeric, specifying sequence length, in codons, used for filtering.

Value

A data.frame containing the computed CAI values for each DNA sequences within df.fasta.

Details

For more information about CAI Sharp and Li, 1987.

Examples

# NOT RUN {
# }
# NOT RUN {
# read DNA from fasta file
fasta <- fasta.read("virus.fasta", "host.fasta")
fasta.v <- fasta[[1]]
fasta.h <- fasta[[2]]
# Calculate CAI
enc.df.host <- ENc.values(fasta.h) 
# }
# NOT RUN {
cai.df <- CAI.values(fasta.v, enc.df.host, fasta.h)


# }