rbind_dry_run.RdThis 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.
rbind_dry_run(
ref,
target,
use_position = FALSE,
flip_strand = FALSE,
quiet = FALSE
)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.
either a gen_tibble object, or the path to the PLINK bim file
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).
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
boolean whether to omit reporting to screen
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)