"transitions": SNPs that are transitions. "transversions": SNPs that are transversions. "syn": synonymous sites. "nonsyn": nonsynonymous sites. "exon": SNPs in exon regions. "intron": SNPs in intron regions. "coding": SNPs in coding regions (CDS). "utr": SNPs in UTR regions. "gene": SNPs in genes.
biallelic.structure
fixed and shared polymorphisms (stored in GENOME.class@region.stats).
mismatch.distribution
statistics based on mismatch distribution
site.spectrum
minor allele frequency of each SNP
site.FST
computes FST for each SNP
Value
The return value is a modified object of class "GENOME"
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The following Slots will be modified in the "GENOME" object
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MDSD
...
MDG1
...
MDG2
...
region.stats
the slot biallelic.structure and minor.allele.freqs will be filled
The function get.detail(GENOME.class, biallelic.structure=TRUE)
returns a matrix for each region, where
0
population is polymorphic, the remaining individuals are polymorphic
1
population is polymorphic, the remaining individuals are monomorphic
2
population is monomorphic, the remaining individuals are polymorphic
3
population is monomorphic, the remaining individuals are monomorphic with the same value
4
population is monomorphic, the remaining individuals are monomorphic with different values