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Merging Format 5 Binary Dosage Files

Introduction

The mergebd function merges two or more Format 5 binary dosage files into a single Format 5 output file. The merge type is detected automatically from the input files.

If both subject IDs and SNP IDs overlap across files an error is returned, since the merge type is ambiguous.

SNPs are identified by chromosome, position, reference allele, and alternate allele, regardless of the SNP ID format stored in each file.

The function takes the following parameters.

Setup

The examples below use the bgzipped VCF file included with the package, set1a.vcf.gz, which contains data for 60 subjects and 10 SNPs on chromosome 1. All output files are written to a temporary directory.

bdose_full <- file.path(tempdir(), "full.bdose")

if (requireNamespace("vcfppR", quietly = TRUE)) {
  vcftobd(vcffile    = system.file("extdata", "set1a.vcf.gz", package = "BinaryDosage"),
          bdose_file = bdose_full)
} else {
  updatebd(bdfiles    = system.file("extdata", "vcf1a.bdose", package = "BinaryDosage"),
           bdose_file = bdose_full)
}
bd_full <- getbdinfo(bdose_full)

cat("Subjects:", nrow(bd_full$samples), "\n")
#> Subjects: 60
cat("SNPs:    ", nrow(bd_full$snps),    "\n")
#> SNPs:     10

Subject merge

A subject merge combines files that cover different subjects but the same (or overlapping) set of SNPs. The output contains all subjects and the SNPs common to every input file.

The example splits the 60-subject file into two 30-subject files using subsetbd, then merges them back together.

bdose_a   <- file.path(tempdir(), "set_a.bdose")
bdose_b   <- file.path(tempdir(), "set_b.bdose")
bdose_out <- file.path(tempdir(), "merged_subjects.bdose")

sids <- bd_full$samples$sid

subsetbd(bdfiles    = bdose_full,
         bdose_file = bdose_a,
         subjectids = sids[1:30])

subsetbd(bdfiles    = bdose_full,
         bdose_file = bdose_b,
         subjectids = sids[31:60])

mergebd(bdose_files = c(bdose_a, bdose_b),
        bdose_file  = bdose_out)

bd_a   <- getbdinfo(bdose_a)
bd_b   <- getbdinfo(bdose_b)
bd_out <- getbdinfo(bdose_out)

cat("File A subjects:", nrow(bd_a$samples),   "\n")
#> File A subjects: 30
cat("File B subjects:", nrow(bd_b$samples),   "\n")
#> File B subjects: 30
cat("Merged subjects:", nrow(bd_out$samples), "\n")
#> Merged subjects: 60
cat("Merged SNPs:    ", nrow(bd_out$snps),    "\n")
#> Merged SNPs:     10

The merged file contains all 60 subjects and all 10 SNPs.

Verifying subject order

The subjects in the merged file appear in input-file order: all subjects from the first file followed by all subjects from the second file.

knitr::kable(bd_out$samples, caption = "Subjects in merged file")
Subjects in merged file
fid sid
I1
I2
I3
I4
I5
I6
I7
I8
I9
I10
I11
I12
I13
I14
I15
I16
I17
I18
I19
I20
I21
I22
I23
I24
I25
I26
I27
I28
I29
I30
I31
I32
I33
I34
I35
I36
I37
I38
I39
I40
I41
I42
I43
I44
I45
I46
I47
I48
I49
I50
I51
I52
I53
I54
I55
I56
I57
I58
I59
I60

SNP merge

A SNP merge combines files that cover different SNPs but the same (or overlapping) set of subjects. The output contains all SNPs and the subjects common to every input file.

The example splits the 10-SNP file into two 5-SNP files using subsetbd, then merges them back together.

bdose_snp_a   <- file.path(tempdir(), "snp_a.bdose")
bdose_snp_b   <- file.path(tempdir(), "snp_b.bdose")
bdose_snp_out <- file.path(tempdir(), "merged_snps.bdose")

locs <- bd_full$snps$location

subsetbd(bdfiles    = bdose_full,
         bdose_file = bdose_snp_a,
         locations  = locs[1:5])

subsetbd(bdfiles    = bdose_full,
         bdose_file = bdose_snp_b,
         locations  = locs[6:10])

mergebd(bdose_files = c(bdose_snp_a, bdose_snp_b),
        bdose_file  = bdose_snp_out)

bd_snp_a   <- getbdinfo(bdose_snp_a)
bd_snp_b   <- getbdinfo(bdose_snp_b)
bd_snp_out <- getbdinfo(bdose_snp_out)

cat("File A SNPs:    ", nrow(bd_snp_a$snps),   "\n")
#> File A SNPs:     5
cat("File B SNPs:    ", nrow(bd_snp_b$snps),   "\n")
#> File B SNPs:     5
cat("Merged SNPs:    ", nrow(bd_snp_out$snps),  "\n")
#> Merged SNPs:     10
cat("Merged subjects:", nrow(bd_snp_out$samples), "\n")
#> Merged subjects: 60

Verifying SNP order

SNPs appear in input-file order: all SNPs from the first file followed by all SNPs from the second file.

knitr::kable(bd_snp_out$snps, caption = "SNPs in merged file")
SNPs in merged file
chromosome location snpid reference alternate
1 10000 1:10000:C:A C A
1 11000 1:11000:T:C T C
1 12000 1:12000:T:C T C
1 13000 1:13000:T:C T C
1 14000 1:14000:G:C G C
1 15000 1:15000:A:C A C
1 16000 1:16000:G:A G A
1 17000 1:17000:C:A C A
1 18000 1:18000:C:G C G
1 19000 1:19000:T:G T G

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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