Calculate nucleotide diversity for each position in the coding sequence
the $dat field of a tidyVCF object
logical, if true, assume all undetermined geneotypes are 0|0 in positions where no 0|0s are present
input with Diversity field appended
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## make a gene info DF geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810")) ## download a single VCF myVCF <- VCFByTranscript(geneInfo[1, ]) ## calculate site-wise nucleotide diversity of a single VCF myVCFWithDiv <- Nucleotide_diversity(myVCF) ## This function can also be applied to a list of VCF files created by the ## `VCFList()` function, see example in the documentation for VCFList()
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