parseEFF: Parse the EFF field of the VCF files from 1001genomes.org

In wrightrc/r1001genomes: Access and analyze the 1001 genomes Arabidopsis resequencing dataset

Description

Parse the EFF field of the VCF files from 1001genomes.org

Usage

parseEFF(tidyVCF)

Arguments

tidyVCF	tidyVCF$dat tibble to be parsed. should have an 'EFF' field
Transcript_ID	Character string of the transcript ID. if NULL, the function will look for it as the attribute "transcript_ID" of the dataframe

Value

new tidyVCF object with added columns for the parsed effect fields

Examples

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

## download a single VCF
myVCF <- VCFByTranscript(geneInfo[1, ])

## Parse the EFF field of a single VCF
myParsedVCF <- parseEFF(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()

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