Skip to contents

Check and export a GRS weights file

Source: R/grs.R
grs_check.Rd

Reads a SNP weights file, validates its content, and writes a plink2-compatible space-delimited output ready for upload to UKB RAP.

Usage

grs_check(file, dest = NULL)

Arguments

file

Character scalar. Path to the input weights file. Read via data.table::fread (format auto-detected; handles CSV, TSV, space-delimited, etc.).

dest

Character scalar or NULL. Output path for the validated, space-delimited weights file. When NULL (default), no file is written and the validated data.table is returned invisibly only.

Value

A data.table with columns snp, effect_allele, and beta, returned invisibly.

Details

The input file must contain at least the three columns below (additional columns are ignored):

snp

SNP identifier, expected in rs + digits format.

effect_allele

Effect allele; must be one of A / T / C / G.

beta

Effect size (log-OR or beta coefficient); must be numeric.

Checks performed:

  • Required columns present.

  • No NA values in the three required columns.

  • No duplicate snp identifiers.

  • snp matches rs[0-9]+ pattern (warning if not).

  • effect_allele contains only A / T / C / G (warning if not).

  • beta is numeric (error if not).

Examples

tmp_in <- tempfile(fileext = ".csv")
weights <- data.frame(
  snp           = c("rs1234567", "rs2345678", "rs3456789"),
  effect_allele = c("A", "T", "G"),
  beta          = c(0.12, -0.05, 0.23)
)
write.csv(weights, tmp_in, row.names = FALSE)

w <- grs_check(tmp_in)
#> Read /tmp/RtmpeYekTR/file230f794ae097.csv: 3 rows, 3 columns.
#> ✔ No NA values.
#> ✔ No duplicate SNPs.
#> ✔ All SNP IDs match rs[0-9]+ format.
#> ✔ All effect alleles are A/T/C/G.
#> Beta summary:
#>   Range : -0.05 to 0.23
#>   Mean |beta|: 0.1333
#>   Positive : 2 (66.7%)
#>   Negative : 1 (33.3%)
#>   Zero : 0
#> ✔ Weights file passed checks: 3 SNPs ready for UKB RAP.
w
#>          snp effect_allele  beta
#>       <char>        <char> <num>
#> 1: rs1234567             A  0.12
#> 2: rs2345678             T -0.05
#> 3: rs3456789             G  0.23

# Save validated weights to a file
tmp_out <- tempfile(fileext = ".txt")
grs_check(tmp_in, dest = tmp_out)
#> Read /tmp/RtmpeYekTR/file230f794ae097.csv: 3 rows, 3 columns.
#> ✔ No NA values.
#> ✔ No duplicate SNPs.
#> ✔ All SNP IDs match rs[0-9]+ format.
#> ✔ All effect alleles are A/T/C/G.
#> Beta summary:
#>   Range : -0.05 to 0.23
#>   Mean |beta|: 0.1333
#>   Positive : 2 (66.7%)
#>   Negative : 1 (33.3%)
#>   Zero : 0
#> ✔ Weights file passed checks: 3 SNPs ready for UKB RAP.
#> ✔ Saved: /tmp/RtmpeYekTR/file230f53bff400.txt