checkCDS: Checks Integrity of CDS Sequence

Description Usage Arguments Details Value Author(s) See Also Examples

Description

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

Usage

1
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. gina@cannarozzi.com

See Also

seqinr statanacoseq ComputeFop

Examples

1
checkCDS(c2s('ATGTGGTACTCCGACTACGGAGGATAA'))

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