Generic harmonisation function

Source: R/harmonise.r

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

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

Value

Dataframe of outcomes

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)