Convert a vector of GL Strings to a data frame with one column per allele

gl_to_df() takes in a character vector of GL Strings, and transforms it into a wide data frame with one row per GL String and one column per allele.

Usage

gl_to_df(glstrings)

Arguments

glstrings

A character vector of GL Strings.

Value

A data frame with the following three columns:

1. glstring_index Counter for each GL String in the vector

2. namespace (e.g. "hla")

3. version_or_date (e.g. "3.29.0" or "2023-05-27")

In addition, the data frame will have one column for every locus/allele found in the GL strings (e.g. A_1, A_2, B_1, B_2, C_1, C_2 for a class I typing).

See also

• gl_to_vec() for the basic conversion of a GL String to a vector

• df_to_gl() for the opposite operation

Examples

glstrings <-
  c(
    "hla#2023#HLA-A*01:01^HLA-B*07:01+HLA-B*08:01^HLA-C*01:01+HLA-C*03:04",
    "hla#2023#HLA-A*02:01+HLA-A*03:01^HLA-B*07:02+HLA-B*08:02^HLA-C*01:02"
  )
gl_to_df(glstrings)
#> # A tibble: 2 × 9
#>   glstring_index namespace version_or_date A_1     A_2   B_1   B_2   C_1   C_2  
#>            <int> <chr>     <chr>           <chr>   <chr> <chr> <chr> <chr> <chr>
#> 1              1 hla       2023            HLA-A*… NA    HLA-… HLA-… HLA-… HLA-…
#> 2              2 hla       2023            HLA-A*… HLA-… HLA-… HLA-… HLA-… NA   

# If your GL Strings are in a data frame with some ID'ing columns that you
# want to keep attached, call `gl_to_df()` on the GL String column in your
# data frame:
typing_df <- tidyr::tibble(
  id = c("001", "002"),
  glstrings = c(
    "hla#2023#HLA-A*01:01:01:01+HLA-A*02:07",
    "hla#2023#HLA-DRB1*03:15:01:01+HLA-DRB1*04:93"
  )
)
typing_df |>
  dplyr::mutate(gl_df = gl_to_df(glstrings)) |> # make the data frame
  tidyr::unnest(gl_df) # combine with your existing data frame
#> # A tibble: 2 × 9
#>   id    glstrings    glstring_index namespace version_or_date A_1   A_2   DRB1_1
#>   <chr> <chr>                 <int> <chr>     <chr>           <chr> <chr> <chr> 
#> 1 001   hla#2023#HL…              1 hla       2023            HLA-… HLA-… NA    
#> 2 002   hla#2023#HL…              2 hla       2023            NA    NA    HLA-D…
#> # ℹ 1 more variable: DRB1_2 <chr>