snp_match {bigsnpr}

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 = 0.2,
  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_" (whether the alleles must be flipped: A <–> T & C <–> G, because on the opposite strand) and "_REV_" (whether alleles must be swapped: ⁠$a0⁠ <–> ⁠$a1⁠, in which case corresponding ⁠$beta⁠ are multiplied by -1). Default is FALSE.

Value

A single data frame with matched variants. Values in column ⁠$beta⁠ are multiplied by -1 for variants with alleles reversed (i.e. swapped). New variable "_NUM_ID_.ss" returns the corresponding row indices of the input sumstats (first argument of this function), and "_NUM_ID_" corresponding to the input info_snp (second argument).

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)
snp_match(sumstats, info_snp, strand_flip = FALSE)