set.synnonsyn-methods: Set synonymous positions for SNP data
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Usage Arguments Value Note Examples

This generic function classifies the observed biallelic positions read from SNP data files into synonymous and non-synonymous SNPs.

1 2	## S4 method for signature 'GENOME' set.synnonsyn(object,ref.chr,save.codons=FALSE)

`object`	an object of class `"GENOME"`
`ref.chr`	the reference chromosome in FASTA format
`save.codons`	save codon changes

The return value is a modified object of class "GENOME" storing
syn/nonsyn informations in the slot GENOME.class@region.data@synonymous
for each SNP. (1=synonymous,0=non-synonymous)
When save.codons is TRUE the SNP related codon changes
are saved in the corresponding slot GENOME.class@region.data@codons.
(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")
# GENOME.class@region.data@synonymous

PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.