set.synnonsyn-methods: Set synonymous positions for SNP data

Description Usage Arguments Value Note Examples

Description

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

Usage

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

Arguments

object

an object of class "GENOME"

ref.chr

the reference chromosome in FASTA format

save.codons

save codon changes

Value

The return value is a modified object of class "GENOME" storing
syn/nonsyn informations in the slot [email protected]@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 [email protected]@codons.
(see also get.codons(), codontable() and codonise64())

Note

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.

Examples

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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 

PopGenome documentation built on May 20, 2018, 5:03 p.m.