Description Usage Arguments Value Examples
Calculate nucleotide diversity for each position in the coding sequence
1 | Nucleotide_diversity(tidyVCF, approxMissingRefGt = TRUE)
|
tidyVCF |
the $dat field of a tidyVCF object |
approxMissingRefGt |
logical, if true, assume all undetermined geneotypes are 0|0 in positions where no 0|0s are present |
input with Diversity field appended
1 2 3 4 5 6 7 8 9 10 11 | ## 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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