Package: BinaryDosage 2.0.0

John Morrison

BinaryDosage: Creates, Merges, and Reads Binary Dosage Files

Tools to create binary dosage files from either VCF or GEN files, merge binary dosage files, and read binary dosage files. Binary dosage files tend to have quicker read times than VCF and GEN formats. There is a small increase in size compared to compressed VCF and GEN files.

Authors:John Morrison [aut, cre], NCI [fnd], NCI [fnd], NIEHS [fnd], NHLBI [fnd]

BinaryDosage_2.0.0.tar.gz
BinaryDosage_2.0.0.zip(r-4.7-x86_64)BinaryDosage_2.0.0.zip(r-4.7-arm64)BinaryDosage_2.0.0.zip(r-4.6-x86_64)BinaryDosage_2.0.0.zip(r-4.6-arm64)
BinaryDosage_2.0.0.tar.gz(r-4.7-arm64)BinaryDosage_2.0.0.tar.gz(r-4.7-x86_64)BinaryDosage_2.0.0.tar.gz(r-4.6-arm64)BinaryDosage_2.0.0.tar.gz(r-4.6-x86_64)
BinaryDosage_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BinaryDosage/json (API)

# Install 'BinaryDosage' in R:
install.packages('BinaryDosage', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

zlibcpp

5.13 score 1 packages 82 scripts 360 downloads 22 exports 37 dependencies

Last updated from:40f112c2b3. Checks:10 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK114
linux-devel-x86_64OK153
source / vignettesOK236
linux-release-arm64OK124
linux-release-x86_64OK157
windows-devel-arm64OK222
windows-devel-x86_64OK169
windows-release-arm64OK242
windows-release-x86_64OK140
wasm-releaseOK1639

Exports:bdapplybdmergeclosebd5congenapplygentobdgetaafgetbd5snpgetbd5snp_bufgetbd5snp_congetbdinfogetgeninfogetmafgetrsqgetsnpgetvcfinfomergebdopenbd5consubsetbdupdatebdvcfapplyvcftobdvcftobdlegacy

Dependencies:clicodetoolscpp11data.tablediagramdigestfarverfuturefuture.applyggplot2globalsgluegtableisobandKernSmoothlabelinglatticelavalifecyclelistenvMatrixnumDerivparallellyprodlimprogressrR6RColorBrewerRcpprlangS7scalesshapeSQUAREMsurvivalvctrsviridisLitewithr

Binary Dosage Formats
Format 1 | Format 1.1 | Format 1.2 | Format 2 | Format 2.1 | Format 2.2 | Format 3 | Format 3.1 and 3.3 | Format 3.2 | Format 3.4 | Format 4 | Format 4.1 and 4.3 | Format 4.2 and 4.4 | Minimizing the data stored
Rendered frombdformats.Rmdusingknitr::rmarkdown

Last update: 2026-04-29
Started: 2020-01-13

Estimating Imputed R-squares
Rendered fromr2estimates.Rmdusingknitr::rmarkdown

Last update: 2026-04-29
Started: 2020-01-13

Genetic File Information
Common section | Binary Dosage Additional Information | VCF File Additional Information | GEN File Additional Information
Rendered fromgeneticfileinfo.Rmdusingknitr::rmarkdown

Last update: 2026-04-29
Started: 2020-01-13

Legacy Binary Dosage Formats (Formats 1-4)
Introduction | Legacy File Formats | Formats 1, 2, and 3 (three-file layout) | Format 1 | Format 2 | Format 3 | Format 4 (single-file layout) | Compressed storage (subformats x.2 and x.4) | Functions Overview | Converting VCF Files | Example files | Basic conversion | Compressed VCF files | Other VCF formats | snpidformat option | bdoptions — calculating per-SNP statistics | Converting GEN Files | Parameters | snpcolumns | impformat | gz | Merging Legacy Binary Dosage Files | Example | Reading Legacy Binary Dosage Files | getbdinfo | bdapply | getsnp | Working Directly with VCF and GEN Files | VCF files | GEN files | Full Workflow Example
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Merging Files
bdmerge
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Last update: 2026-04-29
Started: 2020-01-13

Merging Format 5 Binary Dosage Files
Introduction | Setup | Subject merge | Verifying subject order | SNP merge | Verifying SNP order
Rendered frommergingbd5files.Rmdusingknitr::rmarkdown

Last update: 2026-04-29
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Reading SNPs from Format 5 Files
Introduction | Setup | getbd5snp | Parameters | Return value | Reading a SNP by index | Reading a SNP by ID | Using getbd5snp in a loop | getbd5snp_buf | Important: R copy-on-modify semantics | Example | getbd5snp_con | Workflow | openbd5con | closebd5con | Choosing a reader
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Last update: 2026-04-29
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Using Binary Dosage files
getbdinfo | bdapply | getsnp
Rendered fromusingbdfiles.Rmdusingknitr::rmarkdown

Last update: 2026-04-29
Started: 2020-01-13

Using Format 5 Binary Dosage Files
Introduction | Example files | Converting a VCF file to Format 5 | Loading Format 5 file information | File and format metadata | Sample information | SNP information | Byte offsets | Reading SNP data | Reading a SNP by index | Reading a SNP by ID | Applying a function to all SNPs
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Last update: 2026-04-29
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Using GEN Files
Introduction | GEN file formats | Example files | Converting a GEN file to the Binary Dosage format | Default options | snpcolumns | startcolumn | impformat | chromosome | header parameter | gz | separator | bdfiles | format | subformat | snpidformat | bdoptions | Additional routines | getgeninfo | genapply
Rendered fromusinggenfiles.Rmdusingknitr::rmarkdown

Last update: 2026-04-29
Started: 2020-01-13

Using VCF files
Introduction | Example files | Converting a VCF file to the Binary Dosage format | Minimac files | Uncompressed VCF files | No imputation information file | Using the imputation information file | Compressed VCF files | Checking the files | Other VCF file formats | Other vcftobdlegacy options | format and subformat options | snpidformat | bdoptions | Additional routines | getvcfinfo | vcfapply
Rendered fromusingvcffiles.Rmdusingknitr::rmarkdown

Last update: 2026-04-29
Started: 2020-01-13