Match alleles

Source: R/match-alleles.R

Match alleles between summary statistics and SNP information. Match by ("chr", "a0", "a1") and ("pos" or "rsid"), accounting for possible strand flips and reverse reference alleles (opposite effects).

snp_match(
  sumstats,
  info_snp,
  strand_flip = TRUE,
  join_by_pos = TRUE,
  remove_dups = TRUE,
  match.min.prop = 0.2,
  return_flip_and_rev = FALSE
)

Arguments

sumstats

A data frame with columns "chr", "pos", "a0", "a1" and "beta".
info_snp

A data frame with columns "chr", "pos", "a0" and "a1".
strand_flip

Whether to try to flip strand? (default is TRUE) If so, ambiguous alleles A/T and C/G are removed.
join_by_pos

Whether to join by chromosome and position (default), or instead by rsid.
remove_dups

Whether to remove duplicates (same physical position)? Default is TRUE.
match.min.prop

Minimum proportion of variants in the smallest data to be matched, otherwise stops with an error. Default is 20%.
return_flip_and_rev

Whether to return internal boolean variables "_FLIP_" and "_REV_" (whether the alleles were flipped and/or reversed). Default is FALSE. Values in column $beta are multiplied by -1 for variants with alleles reversed.

Value

A single data frame with matched variants. Values in column $beta are multiplied by -1 for variants with alleles reversed.

See also

snp_modifyBuild

Examples

sumstats <- data.frame(
  chr = 1,
  pos = c(86303, 86331, 162463, 752566, 755890, 758144),
  a0 = c("T", "G", "C", "A", "T", "G"),
  a1 = c("G", "A", "T", "G", "A", "A"),
  beta = c(-1.868, 0.250, -0.671, 2.112, 0.239, 1.272),
  p = c(0.860, 0.346, 0.900, 0.456, 0.776, 0.383)
)

info_snp <- data.frame(
  id = c("rs2949417", "rs115209712", "rs143399298", "rs3094315", "rs3115858"),
  chr = 1,
  pos = c(86303, 86331, 162463, 752566, 755890),
  a0 = c("T", "A", "G", "A", "T"),
  a1 = c("G", "G", "A", "G", "A")
)

snp_match(sumstats, info_snp)

#> 6 variants to be matched.
#> 1 ambiguous SNPs have been removed.
#> 4 variants have been matched; 1 were flipped and 1 were reversed.
#>   chr    pos a0 a1   beta     p _NUM_ID_.ss          id _NUM_ID_
#> 1   1  86303  T  G -1.868 0.860           1   rs2949417        1
#> 2   1  86331  A  G -0.250 0.346           2 rs115209712        2
#> 3   1 162463  G  A -0.671 0.900           3 rs143399298        3
#> 4   1 752566  A  G  2.112 0.456           4   rs3094315        4
snp_match(sumstats, info_snp, strand_flip = FALSE)

#> 6 variants to be matched.
#> 4 variants have been matched; 0 were flipped and 1 were reversed.
#>   chr    pos a0 a1   beta     p _NUM_ID_.ss          id _NUM_ID_
#> 1   1  86303  T  G -1.868 0.860           1   rs2949417        1
#> 2   1  86331  A  G -0.250 0.346           2 rs115209712        2
#> 3   1 752566  A  G  2.112 0.456           4   rs3094315        4
#> 4   1 755890  T  A  0.239 0.776           5   rs3115858        5