This function creates a summary of the merge report generated by
rbind_dry_run()
Usage
# S3 method for class 'rbind_report'
summary(object, ..., ref_label = "reference", target_label = "target")Arguments
- object
a list generated by
rbind_dry_run()- ...
unused (necessary for compatibility with generic function)
- ref_label
the label for the reference dataset (defaults to "reference")
- target_label
the label for the target dataset (defaults to "target")
Examples
example_gt <- 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
report <- rbind_dry_run(
ref = example_gt, target = test_gt,
flip_strand = TRUE, quiet = TRUE
)
# Get the summary
summary(report)
#> harmonising loci between two datasets
#> flip_strand = TRUE ; remove_ambiguous = TRUE
#> -----------------------------
#> dataset: reference
#> number of SNPs: 6 reduced to 2
#> ( 4 are ambiguous, of which 4 were removed)
#> -----------------------------
#> dataset: target
#> number of SNPs: 6 reduced to 2
#> ( 0 were flipped to match the reference set)
#> ( 4 are ambiguous, of which 4 were removed)