Package: bigsnpr 1.12.14

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'))

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:

LD.wiki34 - Long-range LD regions

On CRAN:

big-data bioinformatics memory-mapped-file parallel-computing polygenic-scores population-structure-inference snp-data statistical-methods

81 exports 186 stars 5.88 score 62 dependencies 3 dependents 12 mentions 1.4k scripts 969 downloads

Last updated 15 hours agofrom:202c30cc78. Checks:OK: 7 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 17 2024
R-4.5-win-x86_64	NOTE	Sep 17 2024
R-4.5-linux-x86_64	NOTE	Sep 17 2024
R-4.4-win-x86_64	OK	Sep 17 2024
R-4.4-mac-x86_64	OK	Sep 17 2024
R-4.4-mac-aarch64	OK	Sep 17 2024
R-4.3-win-x86_64	OK	Sep 17 2024
R-4.3-mac-x86_64	OK	Sep 17 2024
R-4.3-mac-aarch64	OK	Sep 17 2024

Exports:as_SFBM bed bed_autoSVD bed_clumping bed_cor bed_counts bed_cprodVec bed_ld_scores bed_MAF bed_pcadapt bed_prodVec bed_projectPCA bed_projectSelfPCA bed_randomSVD bed_scaleBinom bed_tcrossprodSelf CODE_012 CODE_DOSAGE CODE_IMPUTE_PRED coef_to_liab download_1000G download_beagle download_genetic_map download_plink download_plink2 same_ref seq_log snp_ancestry_summary snp_asGeneticPos snp_asGeneticPos2 snp_attach snp_attachExtdata snp_autoSVD snp_beagleImpute snp_clumping snp_cor snp_fake snp_fastImpute snp_fastImputeSimple snp_fst snp_gc snp_getSampleInfos snp_grid_clumping snp_grid_PRS snp_grid_stacking snp_indLRLDR snp_lassosum2 snp_ld_scores snp_ldpred2_auto snp_ldpred2_grid snp_ldpred2_inf snp_ldsc snp_ldsc2 snp_ldsplit snp_MAF snp_manhattan snp_match snp_MAX3 snp_modifyBuild snp_pcadapt snp_plinkIBDQC snp_plinkKINGQC snp_plinkQC snp_plinkRmSamples snp_prodBGEN snp_PRS snp_pruning snp_qq snp_readBed snp_readBed2 snp_readBGEN snp_readBGI snp_save snp_scaleAlpha snp_scaleBinom snp_simuPheno snp_split snp_subset snp_thr_correct snp_writeBed sub_bed

Dependencies:BH bigassertr bigparallelr bigreadr bigsparser bigstatsr bigutilsr bit cli codetools colorspace cowplot data.table DEoptimR digest doParallel doRNG fansi farver ff flock foreach ggplot2 glue gtable isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nabor nlme parallelly pillar pkgconfig ps R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RhpcBLASctl rlang rmio rngtools robustbase roptim RSpectra runonce scales tibble triebeard urltools utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
LD clumping	bed_clumping snp_clumping snp_indLRLDR snp_pruning
Counts	bed_counts
Cross-product with a vector	bed_cprodVec
Allele frequencies	bed_MAF
Product with a vector	bed_prodVec
Projecting PCA	bed_projectPCA
Projecting PCA	bed_projectSelfPCA
Randomized partial SVD	bed_randomSVD
Binomial(2, p) scaling	bed_scaleBinom
tcrossprod / GRM	bed_tcrossprodSelf
Class bed	bed bed-class bed_RC
Class bigSNP	bigSNP bigSNP-class
Liability scale	coef_to_liab
Download 1000G	download_1000G
Download Beagle 4.1	download_beagle
Download a genetic map	download_genetic_map snp_asGeneticPos2
Download PLINK	download_plink download_plink2
Long-range LD regions	LD.wiki34
Determine reference divergence	same_ref
Stacked C+T (SCT)	SCT snp_grid_clumping snp_grid_PRS snp_grid_stacking
Sequence, evenly spaced on a logarithmic scale	seq_log
Estimation of ancestry proportions	snp_ancestry_summary
Interpolate to genetic positions	snp_asGeneticPos
Attach a "bigSNP" from backing files	snp_attach
Attach a "bigSNP" for examples and tests	snp_attachExtdata
Truncated SVD while limiting LD	bed_autoSVD snp_autoSVD
Imputation	snp_beagleImpute
Correlation matrix	bed_cor snp_cor
Fast imputation	snp_fastImpute
Fast imputation	snp_fastImputeSimple
Fixation index (Fst)	snp_fst
Genomic Control	snp_gc
Get sample information	snp_getSampleInfos
lassosum2	snp_lassosum2
LD scores	bed_ld_scores snp_ld_scores
LDpred2	snp_ldpred2_auto snp_ldpred2_grid snp_ldpred2_inf
LD score regression	snp_ldsc snp_ldsc2
Independent LD blocks	snp_ldsplit
MAF	snp_MAF
Manhattan plot	snp_manhattan
Match alleles	snp_match
MAX3 statistic	snp_MAX3
Modify genome build	snp_modifyBuild
Outlier detection	bed_pcadapt snp_pcadapt
Identity-by-descent	snp_plinkIBDQC
Relationship-based pruning	snp_plinkKINGQC
Quality Control	snp_plinkQC
Remove samples	snp_plinkRmSamples
BGEN matrix product	snp_prodBGEN
PRS	snp_PRS
Q-Q plot	snp_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 file	snp_readBGI
Save modifications	snp_save
Binomial(n, p) scaling	snp_scaleAlpha snp_scaleBinom
Simulate phenotypes	snp_simuPheno
Split-parApply-Combine	snp_split
Subset a bigSNP	snp_subset subset.bigSNP
Thresholding and correction	snp_thr_correct
Write PLINK files from a "bigSNP"	snp_writeBed
Replace extension '.bed'	sub_bed