getCodingDiv: produce dataframe of unique variants on the coding sequence

Description Usage Arguments Value Examples

View source: R/VCF_Utils.R

Description

produce dataframe of unique variants on the coding sequence

Usage

1

Arguments

data

tidyVCF with 'EFF' field parsed and 'Diversity' field calculated

Value

a dataframe of unique variants on the coding sequence

Examples

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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)

wrightrc/r1001genomes documentation built on Nov. 20, 2018, 1:22 a.m.