This generic function classifies the observed biallelic positions read from SNP data files into synonymous and non-synonymous SNPs.
an object of class
the reference chromosome in FASTA format
save codon changes
The return value is a modified object of class
syn/nonsyn informations in the slot
for each SNP. (1=synonymous,0=non-synonymous)
TRUE the SNP related codon changes
are saved in the corresponding slot
(see also get.codons(), codontable() and codonise64())
The data has to be read in with a corresponding GFF/GTF file (CDS fields must be specified);
otherwise a correct classification is not possible. The set.synnonsyn() function does
not work for splitted objects e.g produced via sliding.window.transform() or splitting.data().
Note, transcripts which are in the same CDS region but have different reading frames are
are not specified correctly. PopGenome can also handle coding regions on reverse strands. We have used the program SNPeff to validate our results.
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# GENOME.class <- readData("VCF",format="VCF",gffpath="GFF.Folder") # GENOME.class <- set.synnonsyn(GENOME.class,ref.chr="ref.fas") # [email protected]@synonymous
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