Skip to contents

Decode Haplotype Strings to Nucleotide Sequences

Source: R/haplotypes.R
decode_haplotype_strings.Rd

Converts the dosage-encoded haplotype strings produced by extract_haplotypes (e.g. "02110") into nucleotide sequences (e.g. "AGTT?") using the REF and ALT alleles of each SNP in the block.

Usage

decode_haplotype_strings(
  haplotypes,
  snp_info,
  min_freq = 0.01,
  top_n = NULL,
  missing_string = "."
)

Arguments

haplotypes

List from extract_haplotypes.

snp_info

Data frame with columns SNP, CHR, POS, REF, ALT. Must contain all SNPs in the blocks.

min_freq

Minimum haplotype frequency to include. Default 0.01.

top_n

Integer or NULL. Maximum alleles per block. NULL (default) retains all above min_freq.

missing_string

Missing genotype marker. Default ".".

Value

A data frame with columns:

block_id

Block identifier.

CHR

Chromosome.

start_bp, end_bp

Block boundaries.

hap_rank

Rank by frequency (1 = most common).

hap_id

Column name as it appears in the feature matrix.

dosage_string

Raw dosage string e.g. "02110".

nucleotide_sequence

Decoded nucleotide string e.g. "AGTT?".

frequency

Observed frequency across non-missing individuals.

n_carriers

Number of individuals carrying this haplotype (dosage > 0).

snp_positions

Semicolon-separated CHR:POS of each SNP in the block.

snp_alleles

Semicolon-separated REF/ALT for each SNP.

Details

Each character in a haplotype string is the dosage at one SNP in the block:

  • "0" = homozygous REF -> REF nucleotide (e.g. A)

  • "1" = heterozygous -> IUPAC ambiguity code (e.g. R for A/G)

  • "2" = homozygous ALT -> ALT nucleotide (e.g. G)

  • "." = missing -> N

The result is a data frame with one row per unique haplotype allele per block, showing its nucleotide sequence, frequency, and the REF/ALT at each SNP position. This is the most interpretable representation of what each haplotype allele actually encodes biologically.

Examples

data(ldx_geno, ldx_snp_info, ldx_blocks, package = "LDxBlocks")
haps <- extract_haplotypes(ldx_geno, ldx_snp_info, ldx_blocks, min_snps = 3)
decoded <- decode_haplotype_strings(haps, ldx_snp_info)
head(decoded[, c("block_id","hap_rank","dosage_string",
                  "nucleotide_sequence","frequency")])
#>             block_id hap_rank             dosage_string
#> 1 block_1_1000_25027        1 1011121012111011210020110
#> 2 block_1_1000_25027        2 0111021121110121201121101
#> 3 block_1_1000_25027        3 0010010011000010101111000
#> 4 block_1_1000_25027        4 2022222002222002220020220
#> 5 block_1_1000_25027        5 1122122111221112211121211
#> 6 block_1_1000_25027        6 0000020022000020200020000
#>         nucleotide_sequence frequency
#> 1 SCWRRTYAKTSSWARYCMGACCWRG      0.22
#> 2 GSWRGTYMTWSSTRAYCAKWCSWAR      0.14
#> 3 GCWAGYTAKWGCTARCYAKWSSTAG      0.12
#> 4 CCAGATCAGTCGAAGTCCGACCAGG      0.12
#> 5 SSAGRTCMKWCGWRRTCMKWCSARR      0.11
#> 6 GCTAGTTATTGCTAACCAGACCTAG      0.10