VCFList: download and store several VCFs in a list structure, named by...

Description Usage Arguments Value Examples

Description

download and store several VCFs in a list structure, named by their transcirpt ID

Usage

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VCFList(geneInfo, by = "transcript", tidy = TRUE)

Arguments

geneInfo

a geneInfo dataframe as created by the getGeneInfo() function

by

Value

list of VCF objects

Examples

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## first make a gene info DF
geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))

## download and compile a list of VCF files
myVCFList <- VCFList(geneInfo)

## other functions in this package that operate on VCF data can be applied
## to VCFList objects using plyr::llply()
myVCFList <- plyr::llply(myVCFList, parseEFF)
myVCFList <- plyr::llply(myVCFList, Nucleotide_diversity)
myVCFList <- plyr::llply(myVCFList, addAccDetails)

wrightrc/r1001genomes documentation built on Nov. 10, 2019, 12:45 p.m.