labelBySNPs: Label accessions with the variants they contain

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

Description

Label accessions with the variants they contain

Usage

labelBySNPs(data, collapse = TRUE)

Arguments

data	a data frame of variants with a column named "Indiv"
collapse	logicial value, should each accession be a single line?

Value

a df with a single row per accession, with a new column "SNPs" that has a single text string detailing all the variants from data within that accession

Examples

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)

## When using Collapse=TRUE, each accession will be a single row of the output
labelBySNPs(myVCF, collapse=TRUE)[1:3,]

## When using collapse=FALSE, each SNP of each accession will have it's own row.
labelBySNPs(myVCF, collapse=FALSE)[1:3,]

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