Description Usage Arguments Value Examples
produce dataframe of unique variants on the coding sequence
1 |
data |
tidyVCF with 'EFF' field parsed and 'Diversity' field calculated |
a dataframe of unique variants on the coding sequence
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))
## download a single VCF
myVCF <- VCFByTranscript(geneInfo[1, ])
## Parse the EFF field of a single VCF:
myVCF <- parseEFF(myVCF)
## calculate site-wise nucleotide diversity of a single VCF
myVCF <- Nucleotide_diversity(myVCF)
# get unique coding variants with diversity
myCodingVariants <- getCodingDiv(myVCF)
## plot diversity of coding variants
plotCodingDiv(myCodingVariants)
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