Generate a report of what would happen to each SNP in a merge

This function provides an overview of the fate of each SNP in two gen_tibble objects in the case of a merge. Only SNPs found in both objects will be kept. One object is used as a reference, and SNPs in the other dataset will be flipped and/or alleles swapped as needed. SNPs that have different alleles in the two datasets will also be dropped.

Usage

rbind_dry_run(
  ref,
  target,
  use_position = FALSE,
  flip_strand = FALSE,
  quiet = FALSE
)

Arguments

ref: either a gen_tibble object, or the path to the PLINK bim file; the alleles in this objects will be used as template to flip the ones in target and/or swap their order as necessary.
target: either a gen_tibble object, or the path to the PLINK bim file
use_position: boolean of whether a combination of chromosome and position should be used for matching SNPs. By default, rbind uses the locus name, so this is set to FALSE. When using 'use_position=TRUE', make sure chromosomes are coded in the same way in both gen_tibbles (a mix of e.g. 'chr1', '1' or 'chromosome1' can be the reasons if an unexpectedly large number variants are dropped when merging).
flip_strand: boolean on whether strand flipping should be checked to match the two datasets. Ambiguous SNPs (i.e. A/T and C/G) will also be removed. It defaults to FALSE
quiet: boolean whether to omit reporting to screen

Value

a list with two data.frames, named target and ref. Each data.frame has nrow() equal to the number of loci in the respective dataset, a column id with the locus name, and boolean columns to_keep (the valid loci that will be kept in the merge), alleles_mismatched (loci found in both datasets but with mismatched alleles, leading to those loci being dropped), to_flip (loci that need to be flipped to align the two datasets, only found in target data.frame) and to_swap (loci for which the order of alleles needs to be swapped to align the two datasets, target data.frame)