bigsnpr (version 1.6.1)

snp_match: Match alleles

Description

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).

Usage

snp_match(
  sumstats,
  info_snp,
  strand_flip = TRUE,
  join_by_pos = TRUE,
  remove_dups = 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.

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 50%.

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

# NOT RUN {
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)
snp_match(sumstats, info_snp, strand_flip = FALSE)
# }