harmonise: Generic harmonisation function

In MRCIEU/gwasglue: GWAS summary data sources connected to analytical tools

Description

Assumes ref and alt alleles available for target and reference datasets, and uses chr:pos for alignment

Usage

harmonise(
  chr1,
  pos1,
  ref1,
  alt1,
  chr2,
  pos2,
  ref2,
  alt2,
  rsid2 = NULL,
  indel_recode = FALSE,
  strand_flip = FALSE
)

Arguments

chr1	Vector
pos1	Vector
ref1	Vector
alt1	Vector
chr2	Vector
pos2	Vector
ref2	Vector
alt2	Vector
rsid2	Optional vector
indel_recode	=FALSE. If TRUE then attempts to recode D/I
strand_flip	=FALSE. If TRUE then attempts to flip strand when alignment is not otherwise possible

Details

0: stick 1: swap 2: rename indel 3: rename indel and swap 4: flip 5: flip and swap 6: drop (no match) 7: drop (no reference)

Value

Dataframe of outcomes

MRCIEU/gwasglue documentation built on Feb. 15, 2022, 3:25 p.m.