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Merge variant info from two sources with allele-flip-aware matching

Source: R/sumstatsQc.R
mergeVariantInfo.Rd

Merges variant metadata (chromosome, position, ref, alt) from two sources, detecting and correcting allele flips (where alt/ref are swapped). Creates a canonical key from sorted alleles to match across datasets.

Usage

mergeVariantInfo(variants1, variants2, all = TRUE)

Arguments

variants1

A data.frame with columns chrom, pos, alt, ref, or a GRanges with corresponding metadata columns.

variants2

A data.frame or GRanges with the same columns.

all

Logical. If TRUE (default), returns the union of both sets. If FALSE, returns only variants from variants2 (flipped to match variants1's allele orientation).

Value

A data.frame with columns chrom, pos, alt, ref, deduplicated by position and alleles.

Examples

v1 <- data.frame(chrom = "1", pos = 1:3, alt = "A", ref = "G")
v2 <- data.frame(chrom = "1", pos = 2:4, alt = "A", ref = "G")
mergeVariantInfo(v1, v2, all = TRUE)
#> # A tibble: 4 × 4
#>   chrom   pos alt   ref  
#>   <chr> <int> <chr> <chr>
#> 1 1         1 A     G    
#> 2 1         2 A     G    
#> 3 1         3 A     G    
#> 4 1         4 A     G