Description Usage Arguments Value Examples
Some variants in the same individual changed coordinates between studies. These are all indels, so are due to realignment calling the variant at slightly different locations. We can identify the initial position, by finding the variant that is closest to the validation coordinates.
1 | find_matching_sites(row, de_novos)
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row |
dataframe of a single row for a candidate, with columns for person_id, chrom, start_pos, ref_allele |
de_novos |
dataframe of all variants |
boolean vector for sites that match the current row (the current row should match at minimum).
1 2 3 4 5 6 7 8 9 10 11 12 | sample = 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",
stringsAsFactors=FALSE)
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)
find_matching_sites(sample, variants)
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