Match alleles

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,
  match.min.prop = 0.5
)

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.
match.min.prop	Minimum proportion of variants in the smallest data to be matched, otherwise stops with an error. Default is 50%.

Value

A single data frame with matched variants.

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