checkCDS: Checks Integrity of CDS Sequence

In fredysiegrist/statanacoseq: Statistical Analyses of Codon Usage in Custom Genome Sequences

Description

checkCDS Checks that the character number in the cds is in codons (modulo 3 = zero)

Usage

checkCDS(cds, ignore = FALSE)

Arguments

cds	Sequence to be checked # may be implemented as list List of Coding Sequences as read.fasta input
ignore	If TRUE returns TRUE even in case of biological violations (as for stop codons in sequence).

Details

Based on early codon usage mesures proposed by Ikemura 1981. Original implementation from Alexander Roth 2005-2007, first of several indices for codon usage.

Value

TRUE if all checks are passed with or without warnings, FALSE if an violation is found

Author(s)

Siegrist, F. and Cannarozzi, G. M. [e-mail]

See Also

seqinr statanacoseq ComputeFop

Examples

checkCDS(c2s('ATGTGGTACTCCGACTACGGAGGATAA'))

fredysiegrist/statanacoseq documentation built on May 16, 2019, 2:44 p.m.