Description Usage Arguments Value Examples
Genomic coordinates can be encoded in a variety of ways, this function cleans up coordinates where one column
1 | fix_coordinates_with_allele(variants, coordinate_column, allele_column)
|
variants |
data frame of variants |
coordinate_column |
name of column containing chromosome information |
allele_column |
name of column containing allele information |
a data frame with chrom, start_pos, end_pos and allele columns.
1 2 3 4 5 6 7 8 9 10 | fix_coordinates_with_allele(data.frame(coord=c("chr1:10000"),
allele=c("A/G")), "coord", "allele")
fix_coordinates_with_allele(data.frame(coord=c("chr1:10000"),
allele=c("ATGC/G")), "coord", "allele")
fix_coordinates_with_allele(data.frame(coord=c("chr1:10000"),
allele=c("sub(G->T)")), "coord", "allele")
fix_coordinates_with_allele(data.frame(coord=c("chr1:10000"),
allele=c("del(1)")), "coord", "allele")
fix_coordinates_with_allele(data.frame(coord=c("chr1:10000"),
allele=c("ins(ATG)")), "coord", "allele")
|
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