Check Reference Genome and SNP List Compatibility

Source: R/snp_relevant_functions.R

This function verifies that the reference nucleotides in the SNP list match the corresponding positions in the reference genome. It is used to ensure that the reference genome and SNP list are compatible before introducing SNPs into the genome.

check_ref_snp_match(seg_names, snp_list, ref_genome)

Arguments

seg_names

Character vector of segment/chromosome names to check

snp_list

A nested list where first level contains segment names and second level contains a data frame named 'all', which includes all SNPs having at least POS and REF columns

ref_genome

A DNAStringSet or similar object containing reference sequences, with names matching seg_names

Value

No return value, called for side effects:

  • Prints confirmation message for each matching segment

  • Issues warning if mismatches are found

Details

The function performs the following steps for each segment:

  1. Creates an IRanges object from SNP positions

  2. Extracts reference sequences at those positions

  3. Compares extracted sequences with SNP reference alleles

  4. Reports matches/mismatches via messages and warnings

Examples

if (FALSE) { # \dontrun{
# Example reference genome
ref_genome <- DNAStringSet(c(
  chr1 = "ACTGACTGACTG",
  chr2 = "GTCAGTCAGTCA"
))

# Example SNP list
snp_list <- list(
  chr1 = list(all = data.frame(POS = c(1,5), REF = c("A","C"))),
  chr2 = list(all = data.frame(POS = c(2,6), REF = c("T","T")))
)

check_ref_snp_match(c("chr1", "chr2"), snp_list, ref_genome)
} # }