rbind.gen_tbl: Combine two gen_tibbles

In tidypopgen: Tidy Population Genetics

Combine two gen_tibbles

Description

This function combined two gen_tibbles. By defaults, it subsets the loci and swaps ref and alt alleles to make the two datasets compatible (this behaviour can be switched off with as_is). The first 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 (i.e. triallelic) will also be dropped. There are also options (NOT default) to attempt strand flipping to match alleles (often needed in human datasets from different SNP chips), and remove ambiguous alleles (C/G and A/T) where the correct strand can not be guessed.

Usage

## S3 method for class 'gen_tbl'
rbind(
  ...,
  as_is = FALSE,
  flip_strand = FALSE,
  use_position = FALSE,
  quiet = FALSE,
  backingfile = NULL
)

Arguments

...	two gen_tibble objects. Note that this function can not take more objects, rbind has to be done sequentially for large sets of objects.
as_is	boolean determining whether the loci should be left as they are before merging. If FALSE (the defaults), rbind will attempt to subset and swap alleles as needed.
flip_strand	boolean on whether strand flipping should be checked to match the two datasets. If this is set to TRUE, ambiguous SNPs (i.e. A/T and C/G) will also be removed. It defaults to FALSE
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).
quiet	boolean whether to omit reporting to screen
backingfile	the path and prefix of the files used to store the merged data (it will be a .RDS to store the bigSNP object and a .bk file as its backing file for the FBM)

Details

rbind differs from merging data with plink, which swaps the order of allele1 and allele2 according to minor allele frequency when merging datasets. rbind flips and/or swaps alleles according to the reference dataset, not according to allele frequency.

Value

a gen_tibble with the merged data.

Examples

example_gt <- load_example_gt("gen_tbl")

# Create a second gen_tibble to merge
test_indiv_meta <- data.frame(
  id = c("x", "y", "z"),
  population = c("pop1", "pop1", "pop2")
)
test_genotypes <- rbind(
  c(1, 1, 0, 1, 1, 0),
  c(2, 1, 0, 0, 0, 0),
  c(2, 2, 0, 0, 1, 1)
)
test_loci <- data.frame(
  name = paste0("rs", 1:6),
  chromosome = paste0("chr", c(1, 1, 1, 1, 2, 2)),
  position = as.integer(c(3, 5, 65, 343, 23, 456)),
  genetic_dist = as.double(rep(0, 6)),
  allele_ref = c("A", "T", "C", "G", "C", "T"),
  allele_alt = c("T", "C", NA, "C", "G", "A")
)

test_gt <- gen_tibble(
  x = test_genotypes,
  loci = test_loci,
  indiv_meta = test_indiv_meta,
  valid_alleles = c("A", "T", "C", "G"),
  quiet = TRUE
)

# Merge the datasets using rbind
merged_gt <- rbind(ref = example_gt, target = test_gt, flip_strand = TRUE)

merged_gt

tidypopgen documentation built on Aug. 28, 2025, 1:08 a.m.