fix_zaiidi_coordinates: extract genomic coordinates for variants from a dataframe

In jeremymcrae/publishedDeNovos: Published De Novos Dataset from Developmental Disorder Sequencing Studies

Description

Genomic coordinates can be encoded in a variety of ways, this function cleans up coordinates where one column

Usage

fix_zaiidi_coordinates(variants, allele_column)

Arguments

variants	data frame of variants
allele_column	name of column containing allele information

Value

a data frame with chrom, start_pos, end_pos and allele columns.

Examples

fix_zaiidi_coordinates(data.frame(chrom=c("1"), start_pos=c("100000"),
    alleles=c("A/G")), "alleles")
fix_zaiidi_coordinates(data.frame(chrom=c("1"), start_pos=c("100000"),
    alleles=c("-AAAA")), "alleles")
fix_zaiidi_coordinates(data.frame(chrom=c("1"), start_pos=c("100000"),
    alleles=c("+AAAA")), "alleles")

jeremymcrae/publishedDeNovos documentation built on May 19, 2019, 5:08 a.m.