Combine multiple SNPDataLong objects

This function merges a list of SNPDataLong objects, typically representing different SNP panels or datasets, into a single unified SNPDataLong object. It ensures that all genotype matrices have the same set of SNPs (filling missing SNPs with NA), and merges the marker map information while removing duplicate SNP entries.

combineSNPData(lista)

Arguments

lista

A list of SNPDataLong objects to be combined.

Value

A single SNPDataLong object containing the combined genotype matrix, merged map, and a concatenated path string.

Examples

# \donttest{
make_obj <- function(samples, snps) {
  m <- methods::new("SnpMatrix",
                    matrix(as.raw(1:3),
                           nrow = length(samples),
                           ncol = length(snps),
                           dimnames = list(samples, snps)))
  methods::new("SNPDataLong",
               geno = m,
               map  = data.frame(Name = snps,
                                 Chromosome = 1,
                                 Position = seq_along(snps)),
               path = tempfile(),
               xref_path = "chip1")
}
obj1 <- make_obj(c("S1", "S2"), c("SNP1", "SNP2"))
#> Warning: data length [3] is not a sub-multiple or multiple of the number of rows [2]
obj2 <- make_obj(c("S3", "S4"), c("SNP2", "SNP3"))
#> Warning: data length [3] is not a sub-multiple or multiple of the number of rows [2]
combined <- combineSNPData(list(obj1, obj2))
#> Starting SNPDataLong combination...
#> Unified SNP panel with 3 SNPs.
#> Combination complete. Final matrix: 4 samples x 3 SNPs.
# }