Package: bigsnpr 1.12.16

bigsnpr: Analysis of Massive SNP Arrays

Easy-to-use, efficient, flexible and scalable tools for analyzing massive SNP arrays. Privé et al. (2018) <doi:10.1093/bioinformatics/bty185>.

Authors:Florian Privé [aut, cre], Michael Blum [ths], Hugues Aschard [ths], Bjarni Jóhann Vilhjálmsson [ths]

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bigsnpr.pdf |bigsnpr.html✨
bigsnpr/json (API)
NEWS

# Install 'bigsnpr' in R:
install.packages('bigsnpr', repos = c('https://privefl.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/privefl/bigsnpr/issues

Uses libs:
  • openblas– Optimized BLAS
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

big-databioinformaticsmemory-mapped-fileparallel-computingpolygenic-scorespopulation-structure-inferencesnp-datastatistical-methods

11.41 score 187 stars 3 packages 1.3k scripts 1.7k downloads 12 mentions 82 exports 62 dependencies

Last updated 2 months agofrom:b57ef5ba5c. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 24 2024
R-4.5-win-x86_64OKOct 24 2024
R-4.5-linux-x86_64OKOct 24 2024
R-4.4-win-x86_64OKOct 24 2024
R-4.4-mac-x86_64OKOct 24 2024
R-4.4-mac-aarch64OKOct 24 2024
R-4.3-win-x86_64OKOct 24 2024
R-4.3-mac-x86_64OKOct 24 2024
R-4.3-mac-aarch64OKOct 24 2024

Exports:as_SFBMbedbed_autoSVDbed_clumpingbed_corbed_countsbed_cprodVecbed_ld_scoresbed_MAFbed_pcadaptbed_prodVecbed_projectPCAbed_projectSelfPCAbed_randomSVDbed_scaleBinombed_tcrossprodSelfCODE_012CODE_DOSAGECODE_IMPUTE_PREDcoef_to_liabdownload_1000Gdownload_beagledownload_genetic_mapdownload_plinkdownload_plink2same_refseq_logsnp_ancestry_summarysnp_asGeneticPossnp_asGeneticPos2snp_attachsnp_attachExtdatasnp_autoSVDsnp_beagleImputesnp_clumpingsnp_corsnp_fakesnp_fastImputesnp_fastImputeSimplesnp_fstsnp_gcsnp_getSampleInfossnp_grid_clumpingsnp_grid_PRSsnp_grid_stackingsnp_indLRLDRsnp_lassosum2snp_ld_scoressnp_ldpred2_autosnp_ldpred2_gridsnp_ldpred2_infsnp_ldscsnp_ldsc2snp_ldsplitsnp_MAFsnp_manhattansnp_matchsnp_MAX3snp_modifyBuildsnp_pcadaptsnp_plinkIBDQCsnp_plinkKINGQCsnp_plinkQCsnp_plinkRmSamplessnp_prodBGENsnp_projectSelfPCAsnp_PRSsnp_pruningsnp_qqsnp_readBedsnp_readBed2snp_readBGENsnp_readBGIsnp_savesnp_scaleAlphasnp_scaleBinomsnp_simuPhenosnp_splitsnp_subsetsnp_thr_correctsnp_writeBedsub_bed

Dependencies:BHbigassertrbigparallelrbigreadrbigsparserbigstatsrbigutilsrbitclicodetoolscolorspacecowplotdata.tableDEoptimRdigestdoParalleldoRNGfansifarverffflockforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnabornlmeparallellypillarpkgconfigpsR6RColorBrewerRcppRcppArmadilloRcppEigenRhpcBLASctlrlangrmiorngtoolsrobustbaseroptimRSpectrarunoncescalestibbletriebeardurltoolsutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
LD clumpingbed_clumping snp_clumping snp_indLRLDR snp_pruning
Countsbed_counts
Cross-product with a vectorbed_cprodVec
Allele frequenciesbed_MAF
Product with a vectorbed_prodVec
Projecting PCAbed_projectPCA
Projecting PCAbed_projectSelfPCA snp_projectSelfPCA
Randomized partial SVDbed_randomSVD
Binomial(2, p) scalingbed_scaleBinom
tcrossprod / GRMbed_tcrossprodSelf
Class bedbed bed-class bed_RC
Class bigSNPbigSNP bigSNP-class
Liability scalecoef_to_liab
Download 1000Gdownload_1000G
Download Beagle 4.1download_beagle
Download a genetic mapdownload_genetic_map snp_asGeneticPos2
Download PLINKdownload_plink download_plink2
Long-range LD regionsLD.wiki34
Determine reference divergencesame_ref
Stacked C+T (SCT)SCT snp_grid_clumping snp_grid_PRS snp_grid_stacking
Sequence, evenly spaced on a logarithmic scaleseq_log
Estimation of ancestry proportionssnp_ancestry_summary
Interpolate to genetic positionssnp_asGeneticPos
Attach a "bigSNP" from backing filessnp_attach
Attach a "bigSNP" for examples and testssnp_attachExtdata
Truncated SVD while limiting LDbed_autoSVD snp_autoSVD
Imputationsnp_beagleImpute
Correlation matrixbed_cor snp_cor
Fast imputationsnp_fastImpute
Fast imputationsnp_fastImputeSimple
Fixation index (Fst)snp_fst
Genomic Controlsnp_gc
Get sample informationsnp_getSampleInfos
lassosum2snp_lassosum2
LD scoresbed_ld_scores snp_ld_scores
LDpred2snp_ldpred2_auto snp_ldpred2_grid snp_ldpred2_inf
LD score regressionsnp_ldsc snp_ldsc2
Independent LD blockssnp_ldsplit
MAFsnp_MAF
Manhattan plotsnp_manhattan
Match allelessnp_match
MAX3 statisticsnp_MAX3
Modify genome buildsnp_modifyBuild
Outlier detectionbed_pcadapt snp_pcadapt
Identity-by-descentsnp_plinkIBDQC
Relationship-based pruningsnp_plinkKINGQC
Quality Controlsnp_plinkQC
Remove samplessnp_plinkRmSamples
BGEN matrix productsnp_prodBGEN
PRSsnp_PRS
Q-Q plotsnp_qq
Read PLINK files into a "bigSNP"snp_readBed snp_readBed2
Read BGEN files into a "bigSNP"snp_readBGEN
Read variant info from one BGI filesnp_readBGI
Save modificationssnp_save
Binomial(n, p) scalingsnp_scaleAlpha snp_scaleBinom
Simulate phenotypessnp_simuPheno
Split-parApply-Combinesnp_split
Subset a bigSNPsnp_subset subset.bigSNP
Thresholding and correctionsnp_thr_correct
Write PLINK files from a "bigSNP"snp_writeBed
Replace extension '.bed'sub_bed