VCFByTranscript: download VCF, optionally in tidyVCF format

Description Usage Arguments Value Examples

View source: R/VCF_Utils.R

Description

download VCF, optionally in tidyVCF format

Usage

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VCFByTranscript(geneInfo, strains = NULL, tidy = TRUE,
  dataOnly = TRUE)

Arguments

geneInfo

single row of geneInfo dataframe

strains

numeric vector of strain/ecotypes to include

tidy

logical, if true VCF will be provided in tidyVCF format, see vcfR documentation

dataOnly

logical, if true only return the $dat field of the VCF, (drop the metadata)

Value

the VCF, in the format as requested by the parameters of the function

Examples

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

## download a single VCF
myVCF <- VCFByTranscript(geneInfo)

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