remove_duplicates: remove duplicate variants from the same individual

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

Description

The autism de novos come from multiple studies. Some probands are in multiple studies, so we have to remove duplicate entries, while accounting for potential differences in sample IDs, and possibly different coordinates (for indels).

Usage

remove_duplicates(de_novos)

Arguments

de_novos

dataframe of variants

Value

dataframe of variants, without duplicates

Examples

variants = read.table(header=TRUE, text="
    person_id    chrom start_pos ref_allele alt_allele consequence        study_phenotype
    sample_01    1     10000     AAA        A          frameshift_variant autism
    sample_01.p1 1     10001     AAA        A          frameshift_variant normal_iq_autism
    sample_02    1     10001     AAA        A          frameshift_variant normal_iq_autism",
    stringsAsFactors=FALSE)
remove_duplicates(variants)

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