variantCounts: counts number of variants in certain affect categories use...

Description Usage Arguments Value Examples

View source: R/VCF_Utils.R

Description

counts number of variants in certain affect categories use with plyr::ldply() on VCFList objects to create a table.

Usage

1

Arguments

data

tidyVCF with 'EFF' field parsed

unique

logical, if true only unique variants will be counted

Value

a single row dataframe with variant counts

Examples

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geneInfo <- getGeneInfo(genes = c("AT3G62980", "AT3G26810"))

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

## tabultate unique variants
plyr::ldply(myVCFList, variantCounts, unique=TRUE, .id="transcript_ID")

# tabulate total counts of variants relative to the reference sequence.
plyr::ldply(myVCFList, variantCounts, unique=TRUE, .id="transcript_ID")

wrightrc/r1001genomes documentation built on Sept. 11, 2018, 1:40 a.m.