Liftover genomic coordinates from one genome build to another.

This function allows users to lift genomic co-ordinates from one genome build to another. It uses an over.chain liftOver conversion file. Conversion files can be downloaded from UCSC.

liftover_coord(df, path_to_chain)

Arguments

df	a data.frame object with genomic coordinates. Must include the following columns: CHR - character() vector, with "chr" attached to the chromosome e.g. chr1 BP - base pair, as a numeric() vector Any additional columns included will be preserved.
path_to_chain	a character() vector, with the file path to the UCSC chain file for transformation.

Value

Dataframe with coordinates in different genome build.

Examples

file_path <-
    system.file(
        "testdata",
        "liftover_test_data.txt",
        package = "rutils",
        mustWork = TRUE
    )

hg19_path <-
    system.file(
        "testdata",
        "hg19ToHg38.over.chain",
        package = "rutils",
        mustWork = TRUE
    )

genomic_df <-
    readr::read_delim(file_path,
        delim = " ",
        col_types =
            readr::cols(
                SNP = readr::col_character(),
                CHR = readr::col_factor(),
                BP_hg19 = readr::col_integer(),
                BP_hg38 = readr::col_integer()
            )
    )

liftover_coord(
    df =
        genomic_df %>%
            dplyr::select(SNP,
                CHR,
                BP = BP_hg19
            ),
    path_to_chain = hg19_path
)
#> # A tibble: 10 x 3
#>    CHR          BP SNP       
#>    <chr>     <int> <chr>     
#>  1 9      68413211 rs2639606 
#>  2 6      25056560 rs75264089
#>  3 11      5842331 rs73396229
#>  4 13     94507628 rs55871206
#>  5 2     208036470 rs10932221
#>  6 4     176727425 rs56219727
#>  7 7      81365934 rs73709730
#>  8 1      78612399 rs55838886
#>  9 5        820966 rs3734153 
#> 10 11    130258442 rs79381275